diff --git a/.codespellrc b/.codespellrc deleted file mode 100644 index a38689dfe..000000000 --- a/.codespellrc +++ /dev/null @@ -1,8 +0,0 @@ -[codespell] -# in principle .ipynb can be corrected -- a good number of typos there -# nwb-schema -- excluding since submodule, should have its own fixes/checks -skip = .git,*.pdf,*.svg,venvs,env,nwb-schema -ignore-regex = ^\s*"image/\S+": ".* -# it is optin in a url -# potatos - demanded to be left alone, autogenerated -ignore-words-list = optin,potatos diff --git a/.coveragerc b/.coveragerc deleted file mode 100644 index def839969..000000000 --- a/.coveragerc +++ /dev/null @@ -1,13 +0,0 @@ -[run] -branch = True -source = src/ -omit = - src/pynwb/_version.py - src/pynwb/_due.py - src/pynwb/testing/* - src/pynwb/legacy/* - -[report] -exclude_lines = - pragma: no cover - @abstract diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md index 8a15d5ee2..b7154c83c 100644 --- a/.github/PULL_REQUEST_TEMPLATE/release.md +++ b/.github/PULL_REQUEST_TEMPLATE/release.md @@ -2,10 +2,10 @@ Prepare for release of PyNWB [version] ### Before merging: - [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`, - `requirements-doc.txt`, `requirements-min.txt`, `environment-ros3.yml`, and `setup.py` as needed. + `requirements-doc.txt`, `requirements-min.txt`, and `environment-ros3.yml` as needed. - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`, and any other locations as needed -- [ ] Update `setup.py` as needed +- [ ] Update `pyproject.toml` as needed - [ ] Update `README.rst` as needed - [ ] Update `src/pynwb/nwb-schema` submodule as needed. Check the version number and commit SHA manually - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed diff --git a/.github/workflows/check_sphinx_links.yml b/.github/workflows/check_sphinx_links.yml index e1eddb97a..49da87755 100644 --- a/.github/workflows/check_sphinx_links.yml +++ b/.github/workflows/check_sphinx_links.yml @@ -15,15 +15,15 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.12' - name: Install Sphinx dependencies and package run: | diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index 7aa79c9e7..b7bef25db 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -14,6 +14,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 + - name: Codespell uses: codespell-project/actions-codespell@v2 diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml index f9abba102..2f6cb8619 100644 --- a/.github/workflows/deploy_release.yml +++ b/.github/workflows/deploy_release.yml @@ -10,15 +10,15 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout repo with submodules - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.12' - name: Install build dependencies run: | @@ -28,11 +28,11 @@ jobs: - name: Run tox tests run: | - tox -e py311-upgraded + tox -e py312-upgraded - name: Build wheel and source distribution run: | - tox -e build-py311-upgraded + tox -e build-py312-upgraded ls -1 dist - name: Test installation from a wheel diff --git a/.github/workflows/generate_test_files.yml b/.github/workflows/generate_test_files.yml index 48e33a0b3..27848909b 100644 --- a/.github/workflows/generate_test_files.yml +++ b/.github/workflows/generate_test_files.yml @@ -17,13 +17,13 @@ jobs: - { name: pynwb-1.5.1, pynwb-version: "1.5.1", python-version: "3.8"} - { name: pynwb-2.1.0, pynwb-version: "2.1.0", python-version: "3.9"} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml new file mode 100644 index 000000000..1933fa75e --- /dev/null +++ b/.github/workflows/ruff.yml @@ -0,0 +1,11 @@ +name: Ruff +on: pull_request + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - name: Checkout repo + uses: actions/checkout@v4 + - name: Run ruff + uses: chartboost/ruff-action@v1 diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml index c47941c21..1935c7392 100644 --- a/.github/workflows/run_all_tests.yml +++ b/.github/workflows/run_all_tests.yml @@ -26,23 +26,23 @@ jobs: - { name: linux-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: ubuntu-latest } - { name: linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest } - { name: linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest } - - { name: linux-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: ubuntu-latest } - - { name: linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest } - - { name: linux-python3.11-prerelease , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: ubuntu-latest } + - { name: linux-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest } + - { name: linux-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } + - { name: linux-python3.12-prerelease , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest } - { name: windows-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: windows-latest } - { name: windows-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: windows-latest } - { name: windows-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: windows-latest } - { name: windows-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: windows-latest } - - { name: windows-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: windows-latest } - - { name: windows-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: windows-latest } - - { name: windows-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: windows-latest } + - { name: windows-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: windows-latest } + - { name: windows-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: windows-latest } + - { name: windows-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.11", os: windows-latest } - { name: macos-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: macos-latest } - { name: macos-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: macos-latest } - { name: macos-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: macos-latest } - { name: macos-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: macos-latest } - - { name: macos-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: macos-latest } - - { name: macos-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: macos-latest } - - { name: macos-python3.11-prerelease , test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: macos-latest } + - { name: macos-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: macos-latest } + - { name: macos-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: macos-latest } + - { name: macos-python3.12-prerelease , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: macos-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -50,13 +50,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-ver }} @@ -90,14 +90,14 @@ jobs: matrix: include: - { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } - - { name: linux-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: ubuntu-latest } - - { name: linux-gallery-python3.11-prerelease , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: ubuntu-latest } + - { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } + - { name: linux-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: ubuntu-latest } - { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest } - - { name: windows-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: windows-latest } - - { name: windows-gallery-python3.11-prerelease, test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: windows-latest } + - { name: windows-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: windows-latest } + - { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: windows-latest } - { name: macos-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: macos-latest } - - { name: macos-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded , python-ver: "3.11", os: macos-latest } - - { name: macos-gallery-python3.11-prerelease , test-tox-env: gallery-py311-prerelease, python-ver: "3.11", os: macos-latest } + - { name: macos-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded , python-ver: "3.12", os: macos-latest } + - { name: macos-gallery-python3.12-prerelease , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: macos-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -105,13 +105,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-ver }} @@ -139,9 +139,9 @@ jobs: - { name: conda-linux-python3.9 , test-tox-env: py39 , build-tox-env: build-py39 , python-ver: "3.9" , os: ubuntu-latest } - { name: conda-linux-python3.10 , test-tox-env: py310 , build-tox-env: build-py310 , python-ver: "3.10", os: ubuntu-latest } - { name: conda-linux-python3.11 , test-tox-env: py311 , build-tox-env: build-py311 , python-ver: "3.11", os: ubuntu-latest } - - { name: conda-linux-python3.11-optional , test-tox-env: py311-optional , build-tox-env: build-py311-optional , python-ver: "3.11", os: ubuntu-latest } - - { name: conda-linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest } - - { name: conda-linux-python3.11-prerelease, test-tox-env: py311-prerelease, build-tox-env: build-py311-prerelease, python-ver: "3.11", os: ubuntu-latest } + - { name: conda-linux-python3.12 , test-tox-env: py312 , build-tox-env: build-py312 , python-ver: "3.12", os: ubuntu-latest } + - { name: conda-linux-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } + - { name: conda-linux-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -149,13 +149,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-ver }} @@ -196,9 +196,9 @@ jobs: fail-fast: false matrix: include: - - { name: conda-linux-python3.11-ros3 , python-ver: "3.11", os: ubuntu-latest } - - { name: conda-windows-python3.11-ros3, python-ver: "3.11", os: windows-latest } - - { name: conda-macos-python3.11-ros3 , python-ver: "3.11", os: macos-latest } + - { name: conda-linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest } + - { name: conda-windows-python3.12-ros3, python-ver: "3.12", os: windows-latest } + - { name: conda-macos-python3.12-ros3 , python-ver: "3.12", os: macos-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -206,13 +206,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true activate-environment: ros3 @@ -243,9 +243,9 @@ jobs: fail-fast: false matrix: include: - - { name: conda-linux-gallery-python3.11-ros3 , python-ver: "3.11", os: ubuntu-latest } - - { name: conda-windows-gallery-python3.11-ros3, python-ver: "3.11", os: windows-latest } - - { name: conda-macos-gallery-python3.11-ros3 , python-ver: "3.11", os: macos-latest } + - { name: conda-linux-gallery-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest } + - { name: conda-windows-gallery-python3.12-ros3, python-ver: "3.12", os: windows-latest } + - { name: conda-macos-gallery-python3.12-ros3 , python-ver: "3.12", os: macos-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -253,13 +253,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true activate-environment: ros3 diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml index 18dc00903..400de00f3 100644 --- a/.github/workflows/run_coverage.yml +++ b/.github/workflows/run_coverage.yml @@ -24,7 +24,7 @@ jobs: os: [ubuntu-latest, macos-latest, windows-latest] env: OS: ${{ matrix.os }} - PYTHON: '3.11' + PYTHON: '3.12' steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -32,13 +32,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ env.PYTHON }} @@ -63,11 +63,13 @@ jobs: python -m coverage report -m - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: flags: unit files: coverage.xml fail_ci_if_error: true + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - name: Run integration tests and generate coverage report run: | diff --git a/.github/workflows/run_dandi_read_tests.yml b/.github/workflows/run_dandi_read_tests.yml index 7148d209e..df9ef4613 100644 --- a/.github/workflows/run_dandi_read_tests.yml +++ b/.github/workflows/run_dandi_read_tests.yml @@ -17,15 +17,15 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.12' - name: Install run dependencies run: | diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml deleted file mode 100644 index a57042c66..000000000 --- a/.github/workflows/run_flake8.yml +++ /dev/null @@ -1,31 +0,0 @@ -name: Run style check -on: pull_request - -jobs: - run-flake8: - runs-on: ubuntu-latest - steps: - - name: Cancel non-latest runs - uses: styfle/cancel-workflow-action@0.11.0 - with: - all_but_latest: true - access_token: ${{ github.token }} - - - uses: actions/checkout@v3 - with: - submodules: 'recursive' - fetch-depth: 0 # tags are required for versioneer to determine the version - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.11' - - - name: Install flake8 - run: | - python -m pip install --upgrade pip - python -m pip install flake8 - python -m pip list - - - name: Run flake8 - run: flake8 diff --git a/.github/workflows/run_inspector_tests.yml b/.github/workflows/run_inspector_tests.yml index da7efff5f..cb8d57458 100644 --- a/.github/workflows/run_inspector_tests.yml +++ b/.github/workflows/run_inspector_tests.yml @@ -15,15 +15,15 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.12' - name: Update pip run: python -m pip install --upgrade pip diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index e4479a554..d2b3d169a 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -21,9 +21,9 @@ jobs: include: - { name: linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact - - { name: linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest , upload-wheels: true } + - { name: linux-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: ubuntu-latest , upload-wheels: true } - { name: windows-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: windows-latest } - - { name: windows-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: windows-latest } + - { name: windows-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: windows-latest } - { name: macos-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: macos-latest } steps: - name: Cancel non-latest runs @@ -32,13 +32,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-ver }} @@ -79,9 +79,9 @@ jobs: matrix: include: - { name: linux-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } - - { name: linux-gallery-python3.11-upgraded , test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: ubuntu-latest } + - { name: linux-gallery-python3.12-upgraded , test-tox-env: gallery-py312-upgraded, python-ver: "3.12", os: ubuntu-latest } - { name: windows-gallery-python3.8-minimum , test-tox-env: gallery-py38-minimum , python-ver: "3.8" , os: windows-latest } - - { name: windows-gallery-python3.11-upgraded, test-tox-env: gallery-py311-upgraded, python-ver: "3.11", os: windows-latest } + - { name: windows-gallery-python3.12-upgraded, test-tox-env: gallery-py312-upgraded, python-ver: "3.12", os: windows-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -89,13 +89,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-ver }} @@ -120,7 +120,7 @@ jobs: matrix: include: - { name: conda-linux-python3.8-minimum , test-tox-env: py38-minimum , build-tox-env: build-py38-minimum , python-ver: "3.8" , os: ubuntu-latest } - - { name: conda-linux-python3.11-upgraded , test-tox-env: py311-upgraded , build-tox-env: build-py311-upgraded , python-ver: "3.11", os: ubuntu-latest } + - { name: conda-linux-python3.12-upgraded , test-tox-env: py312-upgraded , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: ubuntu-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -128,13 +128,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-ver }} @@ -174,7 +174,7 @@ jobs: fail-fast: false matrix: include: - - { name: conda-linux-python3.11-ros3 , python-ver: "3.11", os: ubuntu-latest } + - { name: conda-linux-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -182,13 +182,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true activate-environment: ros3 @@ -219,7 +219,7 @@ jobs: fail-fast: false matrix: include: - - { name: conda-linux-gallery-python3.11-ros3 , python-ver: "3.11", os: ubuntu-latest } + - { name: conda-linux-gallery-python3.12-ros3 , python-ver: "3.12", os: ubuntu-latest } steps: - name: Cancel non-latest runs uses: styfle/cancel-workflow-action@0.11.0 @@ -227,13 +227,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Conda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true activate-environment: ros3 @@ -271,15 +271,15 @@ jobs: access_token: ${{ github.token }} - name: Checkout repo with submodules - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: submodules: 'recursive' fetch-depth: 0 # tags are required for versioneer to determine the version - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.12' - name: Download wheel and source distributions from artifact uses: actions/download-artifact@v3 diff --git a/CHANGELOG.md b/CHANGELOG.md index 06f8a31b3..7da2ccd12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,9 @@ # PyNWB Changelog -## PyNWB 2.6.1 (March 25, 2024) +## PyNWB 2.7.0 (Upcoming) + +### Enhancements and minor changes +- Added support for python 3.12 and upgraded dependency versions. This also includes infrastructure updates for developers. @mavaylon1 [#1853](https://github.com/NeurodataWithoutBorders/pynwb/pull/1853) ### Bug fixes - Fix bug with reading file with linked `TimeSeriesReferenceVectorData` @rly [#1865](https://github.com/NeurodataWithoutBorders/pynwb/pull/1865) diff --git a/MANIFEST.in b/MANIFEST.in index 04c3ad5c8..dd0fdadda 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,4 +1,4 @@ -include license.txt Legal.txt versioneer.py src/pynwb/_version.py src/pynwb/_due.py +include license.txt Legal.txt src/pynwb/_due.py include requirements.txt requirements-dev.txt requirements-doc.txt requirements-min.txt environment-ros3.yml include test.py tox.ini diff --git a/Makefile b/Makefile deleted file mode 100644 index 4005c8915..000000000 --- a/Makefile +++ /dev/null @@ -1,83 +0,0 @@ -PYTHON = python -FLAKE = flake8 -COVERAGE = coverage - -help: - @echo "Please use \`make ' where is one of" - @echo " init to install required packages" - @echo " build to build the python package(s)" - @echo " install to build and install the python package(s)" - @echo " develop to build and install the python package(s) for development" - @echo " test to run all integration and unit tests" - @echo " htmldoc to make the HTML documentation and open it with the default browser" - @echo " coverage to run tests, build coverage HTML report and open it with the default browser" - @echo "" - @echo "Advanced targets" - @echo " apidoc to generate API docs *.rst files from sources" - @echo " coverage-only to run tests and build coverage report" - @echo " coverage-open to open coverage HTML report in the default browser" - @echo " htmlclean to remove all generated documentation" - @echo " htmldoc-only to make the HTML documentation" - @echo " htmldoc-open to open the HTML documentation with the default browser" - @echo " pdfdoc to make the LaTeX sources and build the PDF of the documentation" - -init: - pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt - -build: - $(PYTHON) setup.py build - -install: build - $(PYTHON) setup.py install - -develop: build - $(PYTHON) setup.py develop - -test: - pip install -r requirements-dev.txt - tox - -flake: - $(FLAKE) --exclude=nwb-schema src/ - $(FLAKE) tests/ - $(FLAKE) --ignore E402,W504 docs/gallery - -checkpdb: - find {src,tests} -name "*.py" -exec grep -Hn -e pdb -e breakpoint -e print {} \; - -devtest: - $(PYTHON) test.py - -testclean: - rm *.npy *.nwb *.yaml - -apidoc: - pip install -r requirements-doc.txt - cd docs && $(MAKE) apidoc - -htmldoc-only: apidoc - cd docs && $(MAKE) html - -htmlclean: - cd docs && $(MAKE) clean - -htmldoc-open: - @echo "" - @echo "To view the HTML documentation open: docs/_build/html/index.html" - open docs/_build/html/index.html || xdg-open docs/_build/html/index.html - -htmldoc: htmldoc-only htmldoc-open - -pdfdoc: - cd docs && $(MAKE) latexpdf - @echo "" - @echo "To view the PDF documentation open: docs/_build/latex/PyNWB.pdf" - -coverage-only: - tox -e localcoverage - -coverage-open: - @echo "To view coverage data open: ./tests/coverage/htmlcov/index.html" - open ./tests/coverage/htmlcov/index.html || xdg-open ./tests/coverage/htmlcov/index.html - -coverage: coverage-only coverage-open diff --git a/README.rst b/README.rst index 14eb32fce..d554207cb 100644 --- a/README.rst +++ b/README.rst @@ -13,35 +13,21 @@ Latest Release .. image:: https://anaconda.org/conda-forge/pynwb/badges/version.svg :target: https://anaconda.org/conda-forge/pynwb -Code Coverage -============== - -.. image:: https://github.com/NeurodataWithoutBorders/pynwb/workflows/Run%20coverage/badge.svg - :target: https://github.com/NeurodataWithoutBorders/pynwb/actions?query=workflow%3A%22Run+coverage%22 - -Overall test coverage - -.. image:: https://codecov.io/gh/NeurodataWithoutBorders/pynwb/branch/dev/graph/badge.svg - :target: https://codecov.io/gh/NeurodataWithoutBorders/pynwb - -Unit test coverage - -.. image:: https://codecov.io/gh/NeurodataWithoutBorders/pynwb/branch/dev/graph/badge.svg?flag=unit - :target: https://codecov.io/gh/NeurodataWithoutBorders/pynwb - -Integration test coverage - -.. image:: https://codecov.io/gh/NeurodataWithoutBorders/pynwb/branch/dev/graph/badge.svg?flag=integration - :target: https://codecov.io/gh/NeurodataWithoutBorders/pynwb Overall Health ============== +.. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_coverage.yml/badge.svg + :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_coverage.yml + .. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_tests.yml/badge.svg :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_tests.yml -.. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_flake8.yml/badge.svg - :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_flake8.yml +.. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/codespell.yml/badge.svg + :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/codespell.yml + +.. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/ruff.yml/badge.svg + :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/ruff.yml .. image:: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/check_external_links.yml/badge.svg :target: https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/check_external_links.yml diff --git a/docs/CONTRIBUTING.rst b/docs/CONTRIBUTING.rst index f774f49bf..2ee5d48cb 100644 --- a/docs/CONTRIBUTING.rst +++ b/docs/CONTRIBUTING.rst @@ -115,11 +115,11 @@ Projects are currently used mainly on the NeurodataWithoutBorders organization l .. _sec-styleguides: -Styleguides ------------ +Style Guides +------------ -Git Commit Message Styleguide -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Git Commit Message Style Guide +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Use the present tense ("Add feature" not "Added feature") * The first line should be short and descriptive. @@ -127,8 +127,8 @@ Git Commit Message Styleguide * If a commit fixes an issues, then include "Fix #X" where X is the number of the issue. * Reference relevant issues and pull requests liberally after the first line. -Documentation Styleguide -^^^^^^^^^^^^^^^^^^^^^^^^ +Documentation Style Guide +^^^^^^^^^^^^^^^^^^^^^^^^^ All documentations is written in reStructuredText (RST) using Sphinx. @@ -137,15 +137,31 @@ Did you fix whitespace, format code, or make a purely cosmetic patch in source c Source code changes that are purely cosmetic in nature and do not add anything substantial to the stability, functionality, or testability will generally not be accepted unless they have been approved beforehand. One of the main reasons is that there are a lot of hidden costs in addition to writing the code itself, and with the limited resources of the project, we need to optimize developer time. E.g,. someone needs to test and review PRs, backporting of bug fixes gets harder, it creates noise and pollutes the git repo and many other cost factors. -Format Specification Styleguide -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Format Specification Style Guide +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ **Coming soon** -Python Code Styleguide -^^^^^^^^^^^^^^^^^^^^^^ +Python Code Style Guide +^^^^^^^^^^^^^^^^^^^^^^^ + +Before you create a Pull Request, make sure you are following the PyNWB style guide. +To check whether your code conforms to the PyNWB style guide, simply run the ruff_ tool in the project's root +directory. ``ruff`` will also sort imports automatically and check against additional code style rules. + +We also use ``ruff`` to sort python imports automatically and double-check that the codebase +conforms to PEP8 standards, while using the codespell_ tool to check spelling. + +``ruff`` and ``codespell`` are installed when you follow the developer installation instructions. See +:ref:`install_developers`. + +.. _ruff: https://beta.ruff.rs/docs/ +.. _codespell: https://github.com/codespell-project/codespell + +.. code:: -Python coding style is checked via ``flake8`` for automatic checking of PEP8 style during pull requests. + $ ruff check . + $ codespell Endorsement ----------- diff --git a/docs/gallery/domain/images.py b/docs/gallery/domain/images.py index 58e9a8e8b..135e18c8c 100644 --- a/docs/gallery/domain/images.py +++ b/docs/gallery/domain/images.py @@ -13,7 +13,8 @@ * :py:class:`~pynwb.image.OpticalSeries` for series of images that were presented as stimulus * :py:class:`~pynwb.image.ImageSeries`, for series of images (movie segments); -* :py:class:`~pynwb.image.GrayscaleImage`, :py:class:`~pynwb.image.RGBImage`, :py:class:`~pynwb.image.RGBAImage`, for static images; +* :py:class:`~pynwb.image.GrayscaleImage`, :py:class:`~pynwb.image.RGBImage`, + :py:class:`~pynwb.image.RGBAImage`, for static images; The following examples will reference variables that may not be defined within the block they are used in. For clarity, we define them here: @@ -136,19 +137,23 @@ # External Files # ^^^^^^^^^^^^^^ # -# External files (e.g. video files of the behaving animal) can be added to the :py:class:`~pynwb.file.NWBFile` by creating -# an :py:class:`~pynwb.image.ImageSeries` object using the :py:attr:`~pynwb.image.ImageSeries.external_file` attribute that specifies the -# path to the external file(s) on disk. The file(s) path must be relative to the path of the NWB file. +# External files (e.g. video files of the behaving animal) can be added to the :py:class:`~pynwb.file.NWBFile` +# by creating an :py:class:`~pynwb.image.ImageSeries` object using the +# :py:attr:`~pynwb.image.ImageSeries.external_file` attribute that specifies +# the path to the external file(s) on disk. +# The file(s) path must be relative to the path of the NWB file. # Either ``external_file`` or ``data`` must be specified, but not both. # -# If the sampling rate is constant, use :py:attr:`~pynwb.base.TimeSeries.rate` and :py:attr:`~pynwb.base.TimeSeries.starting_time` to specify time. -# For irregularly sampled recordings, use :py:attr:`~pynwb.base.TimeSeries.timestamps` to specify time for each sample image. +# If the sampling rate is constant, use :py:attr:`~pynwb.base.TimeSeries.rate` and +# :py:attr:`~pynwb.base.TimeSeries.starting_time` to specify time. +# For irregularly sampled recordings, use :py:attr:`~pynwb.base.TimeSeries.timestamps` to specify time for each sample +# image. # # Each external image may contain one or more consecutive frames of the full :py:class:`~pynwb.image.ImageSeries`. # The :py:attr:`~pynwb.image.ImageSeries.starting_frame` attribute serves as an index to indicate which frame # each file contains. -# For example, if the ``external_file`` dataset has three paths to files and the first and the second file have 2 frames, -# and the third file has 3 frames, then this attribute will have values `[0, 2, 4]`. +# For example, if the ``external_file`` dataset has three paths to files and the first and the second file have 2 +# frames, and the third file has 3 frames, then this attribute will have values `[0, 2, 4]`. external_file = [ os.path.relpath(movie_path, nwbfile_path) for movie_path in moviefiles_path diff --git a/docs/gallery/general/extensions.py b/docs/gallery/general/extensions.py index 4ec8f4749..ddf9159c7 100644 --- a/docs/gallery/general/extensions.py +++ b/docs/gallery/general/extensions.py @@ -12,12 +12,6 @@ For a more in-depth, step-by-step guide on how to create, document, and publish NWB extensions, we highly recommend visiting the :nwb_overview:`extension tutorial ` on the :nwb_overview:`nwb overview <>` website. - -.. seealso:: - - For more information on available tools for creating extensions, see - :nwb_overview:`here `. - """ #################### diff --git a/docs/source/conf.py b/docs/source/conf.py index 6b101c23c..6ceee9d50 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -33,8 +33,7 @@ # version is used. sys.path.insert(0, os.path.join(project_root, 'src')) -from pynwb._version import get_versions - +import pynwb # -- Autodoc configuration ----------------------------------------------------- @@ -191,9 +190,9 @@ def __call__(self, filename): # built documents. # # The short X.Y version. -version = '{}'.format(get_versions()['version']) +version = pynwb.__version__ # The full version, including alpha/beta/rc tags. -release = '{}'.format(get_versions()['version']) +release = pynwb.__version__ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/source/install_developers.rst b/docs/source/install_developers.rst index b2c2d18e7..428a7e592 100644 --- a/docs/source/install_developers.rst +++ b/docs/source/install_developers.rst @@ -79,12 +79,12 @@ After you have created and activated a virtual environment, clone the PyNWB git package requirements using the `pip `_ Python package manager, and install PyNWB in editable mode. -.. code:: +.. code:: bash - $ git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git - $ cd pynwb - $ pip install -r requirements.txt - $ pip install -e . + git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git + cd pynwb + pip install -r requirements.txt -r requirements-dev.txt + pip install -e . Run tests @@ -93,31 +93,19 @@ Run tests For running the tests, it is required to install the development requirements. Again, first activate your virtualenv or conda environment. -.. code:: +.. code:: bash - $ git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git - $ cd pynwb - $ pip install -r requirements.txt -r requirements-dev.txt - $ pip install -e . - $ tox + git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/pynwb.git + cd pynwb + pip install -r requirements.txt -r requirements-dev.txt + pip install -e . + tox For debugging it can be useful to keep the intermediate NWB files created by the tests. To keep these files create the environment variables ``CLEAN_NWB``/``CLEAN_HDMF`` and set them to ``1``. -Following PyNWB Style Guide ---------------------------- - -Before you create a Pull Request, make sure you are following PyNWB style guide -(`PEP8 `_). To do that simply run -the following command in the project's root directory. - -.. code:: - - $ flake8 - - FAQ --- diff --git a/environment-ros3.yml b/environment-ros3.yml index 07838258e..155d2a938 100644 --- a/environment-ros3.yml +++ b/environment-ros3.yml @@ -4,18 +4,19 @@ channels: - conda-forge - defaults dependencies: - - python==3.11 - - h5py==3.8.0 + - python==3.12 + - h5py==3.10.0 - hdmf==3.12.2 - - matplotlib==3.7.1 - - numpy==1.24.2 - - pandas==2.0.0 + - matplotlib==3.8.0 + - numpy==1.26 + - pandas==2.1.2 - python-dateutil==2.8.2 - setuptools - - dandi==0.59.0 # NOTE: dandi does not support osx-arm64 - - fsspec==2023.6.0 - - requests==2.28.1 - - aiohttp==3.8.3 + - pytest==7.4.3 # This is for the upcoming pytest update + - dandi==0.60.0 # NOTE: dandi does not support osx-arm64 + - fsspec==2024.2.0 + - requests==2.31.0 + - aiohttp==3.9.3 - pip - pip: - remfile==0.1.9 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..1bae035af --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,111 @@ +[build-system] +requires = ["hatchling", "hatch-vcs"] # hatchling for build | hatch-vcs for versioning +build-backend = "hatchling.build" # the build backend used + +[project] +name = "pynwb" +authors = [ + { name="Andrew Tritt", email="ajtritt@lbl.gov" }, + { name="Ryan Ly", email="rly@lbl.gov" }, + { name="Oliver Ruebel", email="oruebel@lbl.gov" }, + { name="Ben Dichter", email="ben.dichter@gmail.com" }, + { name="Matthew Avaylon", email="mavaylon@lbl.gov" } +] +description= "Package for working with Neurodata stored in the NWB format." +readme = "README.rst" +requires-python = ">=3.8" +license = {text = "BSD-3-Clause"} +classifiers = [ + "Programming Language :: Python", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "License :: OSI Approved :: BSD License", + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "Operating System :: Microsoft :: Windows", + "Operating System :: MacOS", + "Operating System :: Unix", + "Topic :: Scientific/Engineering :: Medical Science Apps." +] +dependencies = [ + "h5py>=2.10", + "hdmf>=3.12.2", + "numpy>=1.18", # match the version used in hdmf + "pandas>=1.1.5", + "python-dateutil>=2.7.3", +] +dynamic = ["version"] # the build backend will compute the version dynamically from git tag (or a __version__) + +[project.optional-dependencies] +# Add optional dependencies here + +[project.urls] +"Homepage" = "https://github.com/NeurodataWithoutBorders/pynwb" +"Bug Tracker" = "https://github.com/NeurodataWithoutBorders/pynwb/issues" + +[tool.hatch.version] +source = "vcs" + +[tool.hatch.build.hooks.vcs] +# this file is created/updated when the package is installed and used in +# src/pynwb/__init__.py to set `__version__` (from _version.py). +version-file = "src/pynwb/_version.py" + +[tool.hatch.build.targets.wheel] +packages = ["src/pynwb"] + +# [tool.pytest.ini_options] # TODO: uncomment when pytest is integrated +# # Addopts creates a shortcut for pytest. For example below, running `pytest` will actually run `pytest --cov --cov-report html`. +# addopts = "--cov --cov-report html" # generates coverage report in html format without showing anything on the terminal. + +[tool.codespell] +skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,nwb-schema,./docs/_build/*,*.ipynb" +ignore-words-list = "optin,potatos" + +[tool.coverage.run] +branch = true +source = ["src/"] +omit = [ + "src/pynwb/_due.py", + "src/pynwb/testing/*", + "src/pynwb/legacy/*" +] + +[tool.coverage.report] +exclude_lines = [ + "pragma: no cover", + "@abstract" +] + +[tool.ruff] +select = ["E", "F", "T100", "T201", "T203"] +exclude = [ + ".git", + ".tox", + "__pycache__", + "build/", + "dist/", + "src/nwb-schema", + "docs/source/conf.py", + "src/pynwb/_due.py", + "test.py" # remove when pytest comes along +] +line-length = 120 + +[tool.ruff.per-file-ignores] +"tests/read_dandi/*" = ["T201"] +"docs/gallery/*" = ["E402", "T201"] +"src/*/__init__.py" = ["F401"] +"src/pynwb/_version.py" = ["T201"] +"src/pynwb/validate.py" = ["T201"] +"scripts/*" = ["T201"] + +# "test_gallery.py" = ["T201"] # Uncomment when test_gallery.py is created + +[tool.ruff.mccabe] +max-complexity = 17 + diff --git a/requirements-dev.txt b/requirements-dev.txt index da53e22bf..173090a57 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -3,12 +3,10 @@ # versions of requirements may be installed due to package incompatibilities. # black==24.3.0 -codespell==2.2.4 -coverage==7.2.2 -flake8==6.0.0 -flake8-debugger==4.1.2 -flake8-print==5.0.0 +codespell==2.2.6 +coverage==7.3.2 +pytest==7.4.3 isort==5.12.0 -pytest==7.1.2 -pytest-cov==4.0.0 -tox==4.4.8 +pytest-cov==4.1.0 +tox==4.11.3 +ruff==0.1.3 diff --git a/requirements-min.txt b/requirements-min.txt index 0e8bde429..f6b765b0b 100644 --- a/requirements-min.txt +++ b/requirements-min.txt @@ -4,4 +4,3 @@ hdmf==3.12.2 numpy==1.18 pandas==1.1.5 python-dateutil==2.7.3 -setuptools diff --git a/requirements.txt b/requirements.txt index ad5d748bd..836052317 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,4 +4,3 @@ hdmf==3.12.2 numpy==1.26.1 pandas==2.1.2 python-dateutil==2.8.2 -setuptools==65.5.1 \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index d44fcc2b1..000000000 --- a/setup.cfg +++ /dev/null @@ -1,42 +0,0 @@ -[versioneer] -VCS = git -versionfile_source = src/pynwb/_version.py -versionfile_build = pynwb/_version.py -tag_prefix = '' -style = pep440-pre - -[flake8] -max-line-length = 120 -max-complexity = 17 -exclude = - .git, - .tox, - __pycache__, - build/, - dist/, - src/pynwb/nwb-schema/ - docs/_build/, - docs/source/conf.py - docs/source/tutorials/ - versioneer.py, - src/pynwb/_version.py - src/pynwb/_due.py -per-file-ignores = - docs/gallery/*:E402,E501,T201 - docs/source/tutorials/*:E402,T201 - src/pynwb/io/__init__.py:F401 - src/pynwb/legacy/io/__init__.py:F401 - tests/integration/__init__.py:F401 - src/pynwb/testing/__init__.py:F401 - src/pynwb/validate.py:T201 - tests/read_dandi/read_first_nwb_asset.py:T201 - setup.py:T201 - test.py:T201 - scripts/*:T201 -extend-ignore = E203 - -[metadata] -description_file = README.rst - -[isort] -profile = black diff --git a/setup.py b/setup.py deleted file mode 100755 index 2a9ecb19e..000000000 --- a/setup.py +++ /dev/null @@ -1,81 +0,0 @@ -# -*- coding: utf-8 -*- - -import sys - -from setuptools import setup, find_packages - -# Some Python installations don't add the current directory to path. -if '' not in sys.path: - sys.path.insert(0, '') - -import versioneer - -with open('README.rst', 'r') as fp: - readme = fp.read() - -pkgs = find_packages('src', exclude=['data']) -print('found these packages:', pkgs) - -schema_dir = 'nwb-schema/core' - -reqs = [ - 'h5py>=2.10', - 'hdmf>=3.12.2', - 'numpy>=1.16', - 'pandas>=1.1.5', - 'python-dateutil>=2.7.3', - 'setuptools' -] - -print(reqs) - -setup_args = { - 'name': 'pynwb', - 'version': versioneer.get_version(), - 'cmdclass': versioneer.get_cmdclass(), - 'description': 'Package for working with Neurodata stored in the NWB format', - 'long_description': readme, - 'long_description_content_type': 'text/x-rst; charset=UTF-8', - 'author': 'Andrew Tritt', - 'author_email': 'ajtritt@lbl.gov', - 'url': 'https://github.com/NeurodataWithoutBorders/pynwb', - 'license': "BSD", - 'install_requires': reqs, - 'packages': pkgs, - 'package_dir': {'': 'src'}, - 'package_data': {'pynwb': ["%s/*.yaml" % schema_dir, "%s/*.json" % schema_dir]}, - 'python_requires': '>=3.8', - 'classifiers': [ - "Programming Language :: Python", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "License :: OSI Approved :: BSD License", - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "Operating System :: Microsoft :: Windows", - "Operating System :: MacOS", - "Operating System :: Unix", - "Topic :: Scientific/Engineering :: Medical Science Apps." - ], - 'keywords': 'Neuroscience ' - 'python ' - 'HDF ' - 'HDF5 ' - 'cross-platform ' - 'open-data ' - 'data-format ' - 'open-source ' - 'open-science ' - 'reproducible-research ' - 'PyNWB ' - 'NWB ' - 'NWB:N ' - 'NeurodataWithoutBorders', - 'zip_safe': False -} - -if __name__ == '__main__': - setup(**setup_args) diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py index 5e29caede..607fe6a9e 100644 --- a/src/pynwb/__init__.py +++ b/src/pynwb/__init__.py @@ -391,8 +391,15 @@ def export(self, **kwargs): from hdmf.data_utils import DataChunkIterator # noqa: F401,E402 from hdmf.backends.hdf5 import H5DataIO # noqa: F401,E402 -from . import _version # noqa: F401,E402 -__version__ = _version.get_versions()['version'] +try: + # see https://effigies.gitlab.io/posts/python-packaging-2023/ + from ._version import __version__ +except ImportError: # pragma: no cover + # this is a relatively slower method for getting the version string + from importlib.metadata import version # noqa: E402 + + __version__ = version("pynwb") + del version from ._due import due, BibTeX # noqa: E402 due.cite( diff --git a/src/pynwb/_version.py b/src/pynwb/_version.py deleted file mode 100644 index bf16355e1..000000000 --- a/src/pynwb/_version.py +++ /dev/null @@ -1,658 +0,0 @@ - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.26 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440-pre" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "None" - cfg.versionfile_source = "src/pynwb/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} diff --git a/src/pynwb/icephys.py b/src/pynwb/icephys.py index 2de21d571..bed2d4ecd 100644 --- a/src/pynwb/icephys.py +++ b/src/pynwb/icephys.py @@ -491,15 +491,15 @@ def __init__(self, **kwargs): if required_dynamic_table_missing: if required_dynamic_table_given[2] < 0: dynamic_table_arg.append(IntracellularResponsesTable) - if not dynamic_table_arg[-1].name in categories_arg: + if dynamic_table_arg[-1].name not in categories_arg: categories_arg.insert(0, dynamic_table_arg[-1].name) if required_dynamic_table_given[1] < 0: dynamic_table_arg.append(IntracellularStimuliTable()) - if not dynamic_table_arg[-1].name in categories_arg: + if dynamic_table_arg[-1].name not in categories_arg: categories_arg.insert(0, dynamic_table_arg[-1].name) if required_dynamic_table_given[0] < 0: dynamic_table_arg.append(IntracellularElectrodesTable()) - if not dynamic_table_arg[-1].name in categories_arg: + if dynamic_table_arg[-1].name not in categories_arg: categories_arg.insert(0, dynamic_table_arg[-1].name) kwargs['category_tables'] = dynamic_table_arg kwargs['categories'] = categories_arg diff --git a/test.py b/test.py old mode 100755 new mode 100644 index 16191ae3f..231facf58 --- a/test.py +++ b/test.py @@ -11,6 +11,7 @@ import sys import traceback import unittest +import importlib.util flags = { 'pynwb': 2, @@ -68,8 +69,11 @@ def run_test_suite(directory, description="", verbose=True): def _import_from_file(script): - import imp - return imp.load_source(os.path.basename(script), script) + modname = os.path.basename(script) + spec = importlib.util.spec_from_file_location(os.path.basename(script), script) + module = importlib.util.module_from_spec(spec) + sys.modules[modname] = module + spec.loader.exec_module(module) warning_re = re.compile("Parent module '[a-zA-Z0-9]+' not found while handling absolute import") diff --git a/tox.ini b/tox.ini index 10b1e0df4..798da6fe6 100644 --- a/tox.ini +++ b/tox.ini @@ -4,7 +4,7 @@ # and then run "tox" from this directory. [tox] -envlist = py38, py39, py310, py311 +envlist = py38, py39, py310, py311, py312 requires = pip >= 22.0 [testenv] @@ -12,7 +12,7 @@ download = True usedevelop = True setenv = PYTHONDONTWRITEBYTECODE = 1 - VIRTUALENV_PIP = 22.3.1 + VIRTUALENV_PIP = 23.3.1 install_command = python -m pip install -U {opts} {packages} @@ -24,41 +24,22 @@ commands = python -m pip list python test.py -v -# Env to create coverage report locally -[testenv:localcoverage] -basepython = python3.11 -commands = - python -m coverage run test.py --pynwb - coverage html -d tests/coverage/htmlcov - -# Test with python 3.11; pinned dev and optional reqs -[testenv:py311-optional] -basepython = python3.11 -install_command = - python -m pip install {opts} {packages} -deps = - -rrequirements-dev.txt - ; -rrequirements-opt.txt -commands = {[testenv]commands} - -# Test with python 3.11; pinned dev and optional reqs; upgraded run reqs -[testenv:py311-upgraded] -basepython = python3.11 +# Test with python 3.12; pinned dev reqs; upgraded run reqs +[testenv:py312-upgraded] +basepython = python3.12 install_command = python -m pip install -U {opts} {packages} deps = -rrequirements-dev.txt - ; -rrequirements-opt.txt commands = {[testenv]commands} -# Test with python 3.11; pinned dev and optional reqs; upgraded, pre-release run reqs -[testenv:py311-prerelease] -basepython = python3.11 +# Test with python 3.12; pinned dev reqs; upgraded, pre-release run reqs +[testenv:py312-prerelease] +basepython = python3.12 install_command = python -m pip install -U --pre {opts} {packages} deps = -rrequirements-dev.txt - ; -rrequirements-opt.txt commands = {[testenv]commands} # Test with python 3.8; pinned dev reqs; minimum run reqs @@ -91,29 +72,24 @@ commands = {[testenv:build]commands} basepython = python3.11 commands = {[testenv:build]commands} -[testenv:build-py311-optional] -basepython = python3.11 -deps = - -rrequirements-dev.txt - ; -rrequirements-opt.txt +[testenv:build-py312] +basepython = python3.12 commands = {[testenv:build]commands} -[testenv:build-py311-upgraded] -basepython = python3.11 +[testenv:build-py312-upgraded] +basepython = python3.12 install_command = python -m pip install -U {opts} {packages} deps = -rrequirements-dev.txt - ; -rrequirements-opt.txt commands = {[testenv:build]commands} -[testenv:build-py311-prerelease] -basepython = python3.11 +[testenv:build-py312-prerelease] +basepython = python3.12 install_command = python -m pip install -U --pre {opts} {packages} deps = -rrequirements-dev.txt - ; -rrequirements-opt.txt commands = {[testenv:build]commands} [testenv:build-py38-minimum] @@ -129,7 +105,7 @@ deps = null commands = python -c "import pynwb" # Envs that will execute gallery tests that do not require ROS3 -# Test with pinned dev, doc, run, and optional reqs +# Test with pinned dev, doc, and run reqs [testenv:gallery] install_command = python -m pip install -U {opts} {packages} @@ -162,9 +138,9 @@ basepython = python3.11 deps = {[testenv:gallery]deps} commands = {[testenv:gallery]commands} -# Test with python 3.11; pinned dev, doc, and optional reqs; upgraded run reqs -[testenv:gallery-py311-upgraded] -basepython = python3.11 +# Test with python 3.12; pinned dev, and doc reqs; upgraded run reqs +[testenv:gallery-py312-upgraded] +basepython = python3.12 deps = -rrequirements-dev.txt commands = @@ -174,9 +150,9 @@ commands = python -m pip list python test.py --example -# Test with python 3.11; pinned dev, doc, and optional reqs; pre-release run reqs -[testenv:gallery-py311-prerelease] -basepython = python3.11 +# Test with python 3.12; pinned dev, doc, and optional reqs; pre-release run reqs +[testenv:gallery-py312-prerelease] +basepython = python3.12 deps = -rrequirements-dev.txt commands = @@ -191,4 +167,4 @@ commands = basepython = python3.8 deps = -rrequirements-min.txt -commands = {[testenv:gallery]commands} \ No newline at end of file +commands = {[testenv:gallery]commands} diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index 223db1d9c..000000000 --- a/versioneer.py +++ /dev/null @@ -1,2194 +0,0 @@ - -# Version: 0.26 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/python-versioneer/python-versioneer -* Brian Warner -* License: Public Domain (Unlicense) -* Compatible with: Python 3.7, 3.8, 3.9, 3.10 and pypy3 -* [![Latest Version][pypi-image]][pypi-url] -* [![Build Status][travis-image]][travis-url] - -This is a tool for managing a recorded version number in setuptools-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -Versioneer provides two installation modes. The "classic" vendored mode installs -a copy of versioneer into your repository. The experimental build-time dependency mode -is intended to allow you to skip this step and simplify the process of upgrading. - -### Vendored mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* run `versioneer install --vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -### Build-time dependency mode - -* `pip install versioneer` to somewhere in your $PATH -* add a `[tool.versioneer]` section to your `pyproject.toml or a - `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) -* add `versioneer` to the `requires` key of the `build-system` table in - `pyproject.toml`: - ```toml - [build-system] - requires = ["setuptools", "versioneer"] - build-backend = "setuptools.build_meta" - ``` -* run `versioneer install --no-vendor` in your source tree, commit the results -* verify version information with `python setup.py version` - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes). - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/python-versioneer/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other languages) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg` and `pyproject.toml`, if necessary, - to include any new configuration settings indicated by the release notes. - See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install --[no-]vendor` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - -## Similar projects - -* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time - dependency -* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of - versioneer -* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools - plugin - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg -[pypi-url]: https://pypi.python.org/pypi/versioneer/ -[travis-image]: -https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg -[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer - -""" -# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring -# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements -# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error -# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with -# pylint:disable=attribute-defined-outside-init,too-many-arguments - -import configparser -import errno -import json -import os -import re -import subprocess -import sys -from pathlib import Path -from typing import Callable, Dict -import functools -try: - import tomli - have_tomli = True -except ImportError: - have_tomli = False - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - my_path = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(my_path)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(my_path), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise OSError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - root = Path(root) - pyproject_toml = root / "pyproject.toml" - setup_cfg = root / "setup.cfg" - section = None - if pyproject_toml.exists() and have_tomli: - try: - with open(pyproject_toml, 'rb') as fobj: - pp = tomli.load(fobj) - section = pp['tool']['versioneer'] - except (tomli.TOMLDecodeError, KeyError): - pass - if not section: - parser = configparser.ConfigParser() - with open(setup_cfg) as cfg_file: - parser.read_file(cfg_file) - parser.get("versioneer", "VCS") # raise error if missing - - section = parser["versioneer"] - - cfg = VersioneerConfig() - cfg.VCS = section['VCS'] - cfg.style = section.get("style", "") - cfg.versionfile_source = section.get("versionfile_source") - cfg.versionfile_build = section.get("versionfile_build") - cfg.tag_prefix = section.get("tag_prefix") - if cfg.tag_prefix in ("''", '""', None): - cfg.tag_prefix = "" - cfg.parentdir_prefix = section.get("parentdir_prefix") - cfg.verbose = section.get("verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - HANDLERS.setdefault(vcs, {})[method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -LONG_VERSION_PY['git'] = r''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.26 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys -from typing import Callable, Dict -import functools - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs, method): # decorator - """Create decorator to mark a method as the handler of a VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) - break - except OSError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%%d" %% (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - with open(versionfile_abs, "r") as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r'\d', r): - continue - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [versionfile_source] - if ipy: - files.append(ipy) - if "VERSIONEER_PEP518" not in globals(): - try: - my_path = __file__ - if my_path.endswith(".pyc") or my_path.endswith(".pyo"): - my_path = os.path.splitext(my_path)[0] + ".py" - versioneer_file = os.path.relpath(my_path) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - with open(".gitattributes", "r") as fobj: - for line in fobj: - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - break - except OSError: - pass - if not present: - with open(".gitattributes", "a+") as fobj: - fobj.write(f"{versionfile_source} export-subst\n") - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.26) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except OSError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces): - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver): - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces): - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(cmdclass=None): - """Get the custom setuptools subclasses used by Versioneer. - - If the package uses a different cmdclass (e.g. one from numpy), it - should be provide as an argument. - """ - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - - cmds = {} if cmdclass is None else cmdclass.copy() - - # we add "version" to setuptools - from setuptools import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # pip install -e . and setuptool/editable_wheel will invoke build_py - # but the build_py command is not expected to copy any files. - - # we override different "build_py" commands for both environments - if 'build_py' in cmds: - _build_py = cmds['build_py'] - else: - from setuptools.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - if getattr(self, "editable_mode", False): - # During editable installs `.py` and data files are - # not copied to build_lib - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if 'build_ext' in cmds: - _build_ext = cmds['build_ext'] - else: - from setuptools.command.build_ext import build_ext as _build_ext - - class cmd_build_ext(_build_ext): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_ext.run(self) - if self.inplace: - # build_ext --inplace will only build extensions in - # build/lib<..> dir with no _version.py to write to. - # As in place builds will already have a _version.py - # in the module dir, we do not need to write one. - return - # now locate _version.py in the new build/ directory and replace - # it with an updated value - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - if not os.path.exists(target_versionfile): - print(f"Warning: {target_versionfile} does not exist, skipping " - "version update. This can happen if you are running build_ext " - "without first running build_py.") - return - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_ext"] = cmd_build_ext - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.setuptools_buildexe import py2exe as _py2exe - except ImportError: - from py2exe.distutils_buildexe import py2exe as _py2exe - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # sdist farms its file list building out to egg_info - if 'egg_info' in cmds: - _sdist = cmds['egg_info'] - else: - from setuptools.command.egg_info import egg_info as _egg_info - - class cmd_egg_info(_egg_info): - def find_sources(self): - # egg_info.find_sources builds the manifest list and writes it - # in one shot - super().find_sources() - - # Modify the filelist and normalize it - root = get_root() - cfg = get_config_from_root(root) - self.filelist.append('versioneer.py') - if cfg.versionfile_source: - # There are rare cases where versionfile_source might not be - # included by default, so we must be explicit - self.filelist.append(cfg.versionfile_source) - self.filelist.sort() - self.filelist.remove_duplicates() - - # The write method is hidden in the manifest_maker instance that - # generated the filelist and was thrown away - # We will instead replicate their final normalization (to unicode, - # and POSIX-style paths) - from setuptools import unicode_utils - normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/') - for f in self.filelist.files] - - manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt') - with open(manifest_filename, 'w') as fobj: - fobj.write('\n'.join(normalized)) - - cmds['egg_info'] = cmd_egg_info - - # we override different "sdist" commands for both environments - if 'sdist' in cmds: - _sdist = cmds['sdist'] - else: - from setuptools.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -OLD_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - -INIT_PY_SNIPPET = """ -from . import {0} -__version__ = {0}.get_versions()['version'] -""" - - -def do_setup(): - """Do main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (OSError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (OSError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except OSError: - old = "" - module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] - snippet = INIT_PY_SNIPPET.format(module) - if OLD_SNIPPET in old: - print(" replacing boilerplate in %s" % ipy) - with open(ipy, "w") as f: - f.write(old.replace(OLD_SNIPPET, snippet)) - elif snippet not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(snippet) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -def setup_command(): - """Set up Versioneer and exit with appropriate error code.""" - errors = do_setup() - errors += scan_setup_py() - sys.exit(1 if errors else 0) - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - setup_command()