Use rye to manage package

.gitignore

@@ -0,0 +1,10 @@
+# Python generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# venv
+.venv

.python-version

@@ -0,0 +1 @@
+3.12.6

pyproject.toml

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+[project]
+name = "tinytopics"
+version = "0.1.0"
+description = "Topic modeling via sum-to-one constrained Poisson non-negative matrix factorization (NMF)"
+authors = [
+    { name = "Nan Xiao", email = "[email protected]" }
+]
+dependencies = [
+    "torch>=2.5.0",
+    "numpy>=2.0.2",
+    "tqdm>=4.66.5",
+    "matplotlib>=3.9.2",
+    "scipy>=1.13.1",
+]
+readme = "README.md"
+requires-python = ">= 3.9"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.rye]
+managed = true
+dev-dependencies = [
+    "black>=24.10.0",
+    "mkdocs>=1.6.1",
+    "mkdocs-material>=9.5.42",
+    "mkdocstrings-python>=1.12.2",
+]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/tinytopics"]

requirements-dev.lock

@@ -0,0 +1,145 @@
+# generated by rye
+# use `rye lock` or `rye sync` to update this lockfile
+#
+# last locked with the following flags:
+#   pre: false
+#   features: []
+#   all-features: false
+#   with-sources: false
+#   generate-hashes: false
+#   universal: false
+
+-e file:.
+babel==2.16.0
+    # via mkdocs-material
+black==24.10.0
+certifi==2024.8.30
+    # via requests
+charset-normalizer==3.4.0
+    # via requests
+click==8.1.7
+    # via black
+    # via mkdocs
+    # via mkdocstrings
+colorama==0.4.6
+    # via griffe
+    # via mkdocs-material
+contourpy==1.3.0
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+filelock==3.16.1
+    # via torch
+fonttools==4.54.1
+    # via matplotlib
+fsspec==2024.10.0
+    # via torch
+ghp-import==2.1.0
+    # via mkdocs
+griffe==1.5.1
+    # via mkdocstrings-python
+idna==3.10
+    # via requests
+jinja2==3.1.4
+    # via mkdocs
+    # via mkdocs-material
+    # via mkdocstrings
+    # via torch
+kiwisolver==1.4.7
+    # via matplotlib
+markdown==3.7
+    # via mkdocs
+    # via mkdocs-autorefs
+    # via mkdocs-material
+    # via mkdocstrings
+    # via pymdown-extensions
+markupsafe==3.0.2
+    # via jinja2
+    # via mkdocs
+    # via mkdocs-autorefs
+    # via mkdocstrings
+matplotlib==3.9.2
+    # via tinytopics
+mergedeep==1.3.4
+    # via mkdocs
+    # via mkdocs-get-deps
+mkdocs==1.6.1
+    # via mkdocs-autorefs
+    # via mkdocs-material
+    # via mkdocstrings
+mkdocs-autorefs==1.2.0
+    # via mkdocstrings
+    # via mkdocstrings-python
+mkdocs-get-deps==0.2.0
+    # via mkdocs
+mkdocs-material==9.5.42
+mkdocs-material-extensions==1.3.1
+    # via mkdocs-material
+mkdocstrings==0.26.2
+    # via mkdocstrings-python
+mkdocstrings-python==1.12.2
+mpmath==1.3.0
+    # via sympy
+mypy-extensions==1.0.0
+    # via black
+networkx==3.2.1
+    # via torch
+numpy==2.0.2
+    # via contourpy
+    # via matplotlib
+    # via scipy
+    # via tinytopics
+packaging==24.1
+    # via black
+    # via matplotlib
+    # via mkdocs
+paginate==0.5.7
+    # via mkdocs-material
+pathspec==0.12.1
+    # via black
+    # via mkdocs
+pillow==11.0.0
+    # via matplotlib
+platformdirs==4.3.6
+    # via black
+    # via mkdocs-get-deps
+    # via mkdocstrings
+pygments==2.18.0
+    # via mkdocs-material
+pymdown-extensions==10.11.2
+    # via mkdocs-material
+    # via mkdocstrings
+pyparsing==3.2.0
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via ghp-import
+    # via matplotlib
+pyyaml==6.0.2
+    # via mkdocs
+    # via mkdocs-get-deps
+    # via pymdown-extensions
+    # via pyyaml-env-tag
+pyyaml-env-tag==0.1
+    # via mkdocs
+regex==2024.9.11
+    # via mkdocs-material
+requests==2.32.3
+    # via mkdocs-material
+scipy==1.13.1
+    # via tinytopics
+setuptools==75.2.0
+    # via torch
+six==1.16.0
+    # via python-dateutil
+sympy==1.13.1
+    # via torch
+torch==2.5.0
+    # via tinytopics
+tqdm==4.66.5
+    # via tinytopics
+typing-extensions==4.12.2
+    # via torch
+urllib3==2.2.3
+    # via requests
+watchdog==5.0.3
+    # via mkdocs

requirements.lock

@@ -0,0 +1,61 @@
+# generated by rye
+# use `rye lock` or `rye sync` to update this lockfile
+#
+# last locked with the following flags:
+#   pre: false
+#   features: []
+#   all-features: false
+#   with-sources: false
+#   generate-hashes: false
+#   universal: false
+
+-e file:.
+contourpy==1.3.0
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+filelock==3.16.1
+    # via torch
+fonttools==4.54.1
+    # via matplotlib
+fsspec==2024.10.0
+    # via torch
+jinja2==3.1.4
+    # via torch
+kiwisolver==1.4.7
+    # via matplotlib
+markupsafe==3.0.2
+    # via jinja2
+matplotlib==3.9.2
+    # via tinytopics
+mpmath==1.3.0
+    # via sympy
+networkx==3.2.1
+    # via torch
+numpy==2.0.2
+    # via contourpy
+    # via matplotlib
+    # via scipy
+    # via tinytopics
+packaging==24.1
+    # via matplotlib
+pillow==11.0.0
+    # via matplotlib
+pyparsing==3.2.0
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.13.1
+    # via tinytopics
+setuptools==75.2.0
+    # via torch
+six==1.16.0
+    # via python-dateutil
+sympy==1.13.1
+    # via torch
+torch==2.5.0
+    # via tinytopics
+tqdm==4.66.5
+    # via tinytopics
+typing-extensions==4.12.2
+    # via torch