Pypi

.gitignore

@@ -44,4 +44,5 @@ workflows/maxquant/out/
 
 # builds
 docs/_*
-docs/source
+docs/source
+build

environment.yml

@@ -8,7 +8,7 @@ channels:
   - fastai
   - plotly
 dependencies:
-  - biopython # Aligner
+  # - biopython # Aligner
   - python=3.8
   - numpy=1.20
   - pandas=1
@@ -71,6 +71,8 @@ dependencies:
   - pytest
   - pytest-cov
   - jupytext
+  - flake8
+  - flake8-bugbear
   - pip:
     - -e .
     - mrmr-selection

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,43 @@
+[metadata]
+name = pimms
+version = attr:vaep.__version__
+description = Imputing (MS-based prote-) omics data using self supervised deep learning models
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/RasmussenLab/pimms
+author = Henry Webel
+author_email = "Henry Webel" <[email protected]>
+license = gpl-3.0
+license_files = LICENSE
+classifiers =
+    License :: OSI Approved :: GPL 3.0 LICENSE
+    Intended Audience :: Proteomics
+    Intended Audience :: Healthcare Industry
+    Intended Audience :: Science/Research
+    Programming Language :: Python :: 3
+    Topic :: Scientific/Engineering :: Bio-Informatics
+[options]
+# package_dir =
+packages = find:
+include_package_data = True
+install_requires =
+    numpy
+    matplotlib
+    pandas>=1.4
+    plotly
+    torch<2
+    scikit-learn>=1.0
+    scipy
+    seaborn
+    fastai
+    omegaconf
+    tqdm
+
+[options.packages.find]
+# where = vaep
+exclude =
+    test*
+
+
+[flake8]
+max_line_length = 120

setup.py

@@ -1,35 +1,2 @@
-from setuptools import setup, find_packages
-setup(
-    name="vaep",
-    version="0.1",
-    packages=find_packages(),
-    # scripts=['say_hello.py'],
-
-    # Project uses reStructuredText, so ensure that the docutils get
-    # installed or upgraded on the target machine
-    install_requires=['docutils>=0.3'],
-
-    package_data={
-        # If any package contains *.txt or *.rst files, include them:
-        '': ['*.txt', '*.rst'],
-        # And include any *.msg files found in the 'hello' package, too:
-        'hello': ['*.msg'],
-    },
-
-    # metadata to display on PyPI
-    author="Henry Webel",
-    author_email="[email protected]",
-    description="Variational Autoencoder for Proteomics data.",
-    keywords="proteomics",
-    # url="http://example.com/HelloWorld/",   # project home page, if any
-    # project_urls={
-    #     "Bug Tracker": "https://bugs.example.com/HelloWorld/",
-    #     "Documentation": "https://docs.example.com/HelloWorld/",
-    #     "Source Code": "https://code.example.com/HelloWorld/",
-    # },
-    # classifiers=[
-    #     'License :: OSI Approved :: Python Software Foundation License'
-    # ]
-
-    # could also include long_description, download_url, etc.
-)
+from setuptools import setup
+setup()

vaep/__init__.py

@@ -20,6 +20,9 @@
 
 from . import nb
 
+__license__ = 'GPLv3'
+__version__ = (0, 0, 1)
+
 ## set some defaults
 class IntArrayFormatter(pf.GenericArrayFormatter):
     def _format_strings(self):