Merge pull request #58 from MannLabs/remove_setup_py

substitute setup.py with pyproject.toml
MannLabs · Jan 16, 2025 · 1b62dff · 1b62dff
2 parents b4e4c5b + ef8b37a
commit 1b62dff
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Showing 22 changed files with 289 additions and 205 deletions.
diff --git a/.github/workflows/nbdev_tests.yml b/.github/workflows/nbdev_tests.yml
@@ -21,16 +21,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
       - name: Test pip installation with all loose dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./loose_pip_install.sh
 
       - name: Unittests
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           conda activate directlfq
           nbdev_test

diff --git a/.github/workflows/quick_tests.yml b/.github/workflows/quick_tests.yml
@@ -21,15 +21,20 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
+      - name: Pytest tests
+        shell: bash -le {0}
+        run: |
+          pip install pytest
+          pytest tests/pytest
       - name: Test pip installation with all stable dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./stable_pip_install.sh
       - name: Run pipeline
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd tests
           . ./run_quicktests.sh
@@ -47,15 +52,20 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
+      - name: Pytest tests
+        shell: bash -le {0}
+        run: |
+          pip install pytest
+          pytest tests/pytest
       - name: Test pip installation with all loose dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./loose_pip_install.sh
       - name: Run pipeline
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd tests
           . ./run_quicktests.sh
diff --git a/.github/workflows/quick_tests_ubuntu.yml b/.github/workflows/quick_tests_ubuntu.yml
@@ -21,16 +21,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
       - name: Test pip installation with stable dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./stable_pip_install.sh
 
       - name: Unittests
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd tests
           . ./run_quicktests.sh
diff --git a/.github/workflows/ratio_tests.yml b/.github/workflows/ratio_tests.yml
@@ -19,16 +19,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
       - name: Test pip installation with stable dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./stable_pip_install.sh
 
       - name: Ratio tests
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd tests
           . ./run_ratio_tests.sh
diff --git a/.github/workflows/unused/all_tests.yml b/.github/workflows/unused/all_tests.yml
@@ -22,15 +22,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: latest
       - name: Conda info
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: conda info
       - name: Test pip installation with all loose dependencies
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd misc
           . ./loose_pip_install.sh
       - name: Unittests
-        shell: bash -l {0}
+        shell: bash -le {0}
         run: |
           cd tests
           . ./run_tests.sh
diff --git a/README.md b/README.md
@@ -86,10 +86,10 @@ pip install "directlfq[stable]"
 
 NOTE: You might need to run `pip install pip==21.0` before installing directlfq like this. Also note the double quotes `"`.
 
-For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=directlfq[stable,development-stable]`) from GitHub with e.g.
+For those who are really adventurous, it is also possible to directly install any branch (e.g. `@development`) with any extras (e.g. `#egg=directlfq[stable,development]`) from GitHub with e.g.
 
 ```bash
-pip install "git+https://github.com/MannLabs/directlfq.git@development#egg=directlfq[stable,development-stable]"
+pip install "git+https://github.com/MannLabs/directlfq.git@development#egg=directlfq[stable,development]"
 ```
 
 ### Developer
@@ -122,7 +122,7 @@ Finally, directlfq and all its [dependencies](requirements) need to be installed
 pip install -e "./directlfq[development,gui]"
 ```
 
-By default this installs loose dependencies (no explicit versioning), although it is also possible to use stable dependencies (e.g. `pip install -e "./directlfq[stable,development-stable]"`).
+By default this installs loose dependencies (no explicit versioning), although it is also possible to use stable dependencies (e.g. `pip install -e "./directlfq[stable,development]"`).
 
 ***By using the editable flag `-e`, all modifications to the [directlfq source code folder](directlfq) are directly reflected when running directlfq. Note that the directlfq folder cannot be moved and/or renamed if an editable version is installed. In case of confusion, you can always retrieve the location of any Python module with e.g. the command `import module` followed by `module.__file__`.***
 

diff --git a/directlfq/__init__.py b/directlfq/__init__.py
@@ -1,45 +1 @@
-#!python
-
-
-__project__ = "directlfq"
-__version__ = "0.3.1-dev0"
-__license__ = "Apache"
-__description__ = "An open-source Python package of the AlphaPept ecosystem"
-__author__ = "Mann Labs"
-__author_email__ = "opensource@alphapept.com"
-__github__ = "https://github.com/MannLabs/directlfq"
-__keywords__ = [
-    "bioinformatics",
-    "software",
-    "AlphaPept ecosystem",
-]
-__python_version__ = ">=3.9"
-__classifiers__ = [
-    # "Development Status :: 1 - Planning",
-    # "Development Status :: 2 - Pre-Alpha",
-    # "Development Status :: 3 - Alpha",
-    # "Development Status :: 4 - Beta",
-     "Development Status :: 5 - Production/Stable",
-    # "Development Status :: 6 - Mature",
-    # "Development Status :: 7 - Inactive"
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: Apache Software License",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-]
-__console_scripts__ = [
-    "directlfq=directlfq.cli:run",
-]
-__urls__ = {
-    "Mann Labs at MPIB": "https://www.biochem.mpg.de/mann",
-    "Mann Labs at CPR": "https://www.cpr.ku.dk/research/proteomics/mann/",
-    "GitHub": __github__,
-    # "ReadTheDocs": None,
-    # "PyPi": None,
-    # "Scientific paper": None,
-}
-__extra_requirements__ = {
-    "development": "requirements_development.txt",
-    "gui": "requirements_gui.txt"
-}
+__version__ = "0.3.1-dev0"
diff --git a/misc/loose_pip_install.sh b/misc/loose_pip_install.sh
@@ -1,5 +1,5 @@
 conda create -n directlfq python=3.9 -y
 conda activate directlfq
-pip install -e '../.[development-stable, gui]'
+pip install -e '../.[development, gui]'
 directlfq
 conda deactivate
diff --git a/misc/stable_pip_install.sh b/misc/stable_pip_install.sh
@@ -1,5 +1,5 @@
 conda create -n directlfq python=3.9 -y
 conda activate directlfq
-pip install -e '../.[stable,development-stable, gui-stable]'
+pip install -e '../.[stable, gui-stable, development]'
 directlfq
 conda deactivate
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,60 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "directlfq"
+requires-python = ">=3.9"
+dynamic = ["version", "dependencies", "optional-dependencies"]
+
+authors = [
+    {name = "Mann Labs", email = "opensource@alphapept.com"}
+]
+description = "An open-source Python package of the AlphaPept ecosystem"
+readme = "README.md"
+keywords = [
+    "LFQ",
+    "label-free quantification",
+    "mass spectrometry",
+    "proteomics",
+    "bioinformatics",
+    "AlphaPept",
+    "AlphaPept ecosystem",
+]
+license = {file = "LICENSE.txt"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    # "Development Status :: 6 - Mature",
+    # "Development Status :: 7 - Inactive"
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.urls]
+
+"Paper preprint" = "https://www.biochem.mpg.de/mann"
+Repository = "https://github.com/MannLabs/directlfq"
+#Documentation = "https://readthedocs.org"
+#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
+Issues = "https://github.com/MannLabs/directlfq/issues"
+"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann"
+
+[tool.setuptools.packages]
+find = {}
+
+[tool.setuptools.dynamic]
+# https://stackoverflow.com/a/73600610
+dependencies = {file = ["requirements/requirements_loose.txt"]}
+optional-dependencies = { stable = { file = ["requirements/requirements.txt",
+] }, gui = { file = [ "requirements/requirements_gui_loose.txt",
+] }, gui-stable = { file = [ "requirements/requirements_gui.txt",
+] }, development = { file = ["requirements/requirements_development.txt"
+] }}
+
+version = {attr = "directlfq.__version__"}
+
+[project.scripts]
+directlfq = "directlfq.cli:run"
diff --git a/release/linux/build_installer_linux.sh b/release/linux/build_installer_linux.sh
@@ -8,8 +8,11 @@ rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
 # Creating the wheel
-python setup.py sdist bdist_wheel
-pip install "dist/directlfq-0.3.1-dev0-py3-none-any.whl[stable,gui]"
+python -m build
+
+# substitute X.Y.Z-devN with X.Y.Z.devN
+WHL_NAME=$(echo "directlfq-0.3.1-dev0-py3-none-any.whl" | sed 's/\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\)-dev\([0-9][0-9]*\)/\1.dev\2/g')
+pip install "dist/${WHL_NAME}[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

diff --git a/release/macos/build_installer_macos.sh b/release/macos/build_installer_macos.sh
@@ -8,8 +8,11 @@ rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
 # Creating the wheel
-python setup.py sdist bdist_wheel
-pip install "dist/directlfq-0.3.1-dev0-py3-none-any.whl[stable,gui]"
+python -m build
+
+# substitute X.Y.Z-devN with X.Y.Z.devN
+WHL_NAME=$(echo "directlfq-0.3.1-dev0-py3-none-any.whl" | sed 's/\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\)-dev\([0-9][0-9]*\)/\1.dev\2/g')
+pip install "dist/${WHL_NAME}[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller