Switch from setup.py to pyproject.toml

.github/actions/build-py/action.yml

@@ -19,8 +19,11 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}/
-        /opt/python/cp38-cp38/bin/python setup.py bdist_wheel
-        /opt/python/cp311-cp311/bin/python setup.py bdist_wheel
+        /opt/python/cp38-cp38/bin/python -m pip install build
+        /opt/python/cp38-cp38/bin/python -m build --wheel --outdir dist
+
+        /opt/python/cp311-cp311/bin/python -m pip install build
+        /opt/python/cp311-cp311/bin/python -m build --wheel --outdir dist
         # Exclude memilio-generation, because its a pure python package, cmake is only used in the build process to retrieve data from cpp
         if [[ -f "CMakeLists.txt" ]] && [ "${{ inputs.package }}" != "generation" ]; then 
           # includes native dependencies in the wheel

.github/actions/test-pylint/action.yml

@@ -17,6 +17,7 @@ runs:
       uses: actions/download-artifact@v4
       with:
         name: python-wheels-${{ inputs.package }}
+        path: pycode/wheelhouse
     - name: Install Python Wheels
       shell: bash
       run: |
@@ -27,8 +28,7 @@ runs:
       shell: bash
       run: |
         cd pycode/memilio-${{ inputs.package }}
-        mkdir -p build_pylint
-        python setup.py pylint
+        python memilio/custom_pylint.py
         pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
     - name: Upload Pylint Report
       uses: actions/upload-artifact@v4

pycode/memilio-epidata/README.rst

@@ -115,8 +115,8 @@ See Installation on how to install all these dependencies automatically.
 Run pylint with the commands
 
 .. code:: sh
-
-    python setup.py pylint
+    
+    memiliopylint
     pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
 
 Pylint report for actual master:

pycode/memilio-epidata/memilio/custom_pylint.py

@@ -0,0 +1,53 @@
+from setuptools import Command, Distribution
+import os
+
+__version__ = '1.0.0'
+
+
+class PylintCommand(Command):
+    """
+    Custom command to run pylint and get a report as html.
+    """
+    description = "Runs pylint and outputs the report as html."
+    user_options = []
+
+    def initialize_options(self):
+        from pylint.reporters.json_reporter import JSONReporter
+        from pylint.reporters.text import ParseableTextReporter, TextReporter
+        from pylint_json2html import JsonExtendedReporter
+
+        self.lint_modules = ["memilio/"]
+        self.out_format = "extendedjson"
+
+        self.REPORTERS = {
+            "parseable": (ParseableTextReporter, "build_pylint/pylint_parseable.txt"),
+            "text": (TextReporter, "build_pylint/pylint.txt"),
+            "json": (JSONReporter, "build_pylint/pylint.json"),
+            "extendedjson": (JsonExtendedReporter, "build_pylint/pylint_extended.json")
+        }
+
+    def finalize_options(self):
+        self.reporter, self.out_file = self.REPORTERS.get(
+            self.out_format)
+
+    def run(self):
+        os.makedirs("build_pylint", exist_ok=True)
+
+        # Run pylint
+        from pylint import lint
+        with open(self.out_file, "w", encoding="utf-8") as report_file:
+            options = ["--rcfile=../pylintrc", *self.lint_modules]
+
+            lint.Run(options, reporter=self.reporter(
+                report_file), do_exit=False)
+
+
+def main():
+    cmd = PylintCommand(dist=Distribution())
+    cmd.initialize_options()
+    cmd.finalize_options()
+    cmd.run()
+
+
+if __name__ == "__main__":
+    main()

pycode/memilio-epidata/pyproject.toml

@@ -0,0 +1,65 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = [ "memilio", "memilio.epidata", "memilio.epidata_test"]
+
+[project]
+name = "memilio-epidata"
+version = "1.0.0"
+readme = "README.rst"
+authors = [{name = "DLR-SC", email = "[email protected]"}]
+maintainers = [{email = "[email protected]"}]
+description = "Part of MEmilio project, reads epidemiological data from different official and unofficial sources."
+requires-python = ">=3.8"
+dependencies = [
+     # pandas 2.0 is minimum for CoW
+    "pandas>=2.0.0",
+    # FutureWarning of pandas that pyarrow will be required in a future release
+    "pyarrow",
+    "matplotlib",
+    "tables",
+    # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
+    "numpy>=1.22,<1.25",
+    "openpyxl",
+    "xlrd",
+    "xlsxwriter",
+    "requests",
+    "pyxlsb",
+    "wget",
+    "twill==3.1",
+    "PyQt6",
+    "python-calamine",
+    "python-magic-bin; sys_platform == 'win32'",
+    "python-magic; sys_platform != 'win32'"
+]
+
+[project.optional-dependencies]
+dev = [
+            # first support of python 3.11 4.6
+            # 5.3.4 has conflicts with openpyxl
+            # 5.3.3 broken
+            "pyfakefs>=4.6,<5.3.3",
+            # coverage 7.0.0 can't find .whl files and breaks CI
+            "coverage>=7.0.1",
+            # pylint 2.16 creates problem with wrapt package version
+            "pylint>=2.13.0,<2.16",
+            "pylint_json2html==0.4.0",
+        ]
+
+[project.urls] 
+Repository = "https://github.com/SciCompMod/memilio"
+Issues = "https://github.com/SciCompMod/memilio/issues"
+
+[project.scripts]
+getcasedata = "memilio.epidata.getCaseData:main"
+getpopuldata = "memilio.epidata.getPopulationData:main"
+getjhdata = "memilio.epidata.getJHData:main"
+getdividata = "memilio.epidata.getDIVIData:main"
+getsimdata = "memilio.epidata.getSimulationData:main"
+cleandata = "memilio.epidata.cleanData:main"
+getcommutermobility = "memilio.epidata.getCommuterMobility:main"
+getvaccinationdata = "memilio.epidata.getVaccinationData:main"
+gethospitalizationdata = "memilio.epidata.getHospitalizationData:main"
+memiliopylint = "memilio.custom_pylint:main"

pycode/memilio-plot/memilio/custom_pylint.py

@@ -0,0 +1,53 @@
+from setuptools import Command, Distribution
+import os
+
+__version__ = '1.0.0'
+
+
+class PylintCommand(Command):
+    """
+    Custom command to run pylint and get a report as html.
+    """
+    description = "Runs pylint and outputs the report as html."
+    user_options = []
+
+    def initialize_options(self):
+        from pylint.reporters.json_reporter import JSONReporter
+        from pylint.reporters.text import ParseableTextReporter, TextReporter
+        from pylint_json2html import JsonExtendedReporter
+
+        self.lint_modules = ["memilio/"]
+        self.out_format = "extendedjson"
+
+        self.REPORTERS = {
+            "parseable": (ParseableTextReporter, "build_pylint/pylint_parseable.txt"),
+            "text": (TextReporter, "build_pylint/pylint.txt"),
+            "json": (JSONReporter, "build_pylint/pylint.json"),
+            "extendedjson": (JsonExtendedReporter, "build_pylint/pylint_extended.json")
+        }
+
+    def finalize_options(self):
+        self.reporter, self.out_file = self.REPORTERS.get(
+            self.out_format)
+
+    def run(self):
+        os.makedirs("build_pylint", exist_ok=True)
+
+        # Run pylint
+        from pylint import lint
+        with open(self.out_file, "w", encoding="utf-8") as report_file:
+            options = ["--rcfile=../pylintrc", *self.lint_modules]
+
+            lint.Run(options, reporter=self.reporter(
+                report_file), do_exit=False)
+
+
+def main():
+    cmd = PylintCommand(dist=Distribution())
+    cmd.initialize_options()
+    cmd.finalize_options()
+    cmd.run()
+
+
+if __name__ == "__main__":
+    main()

pycode/memilio-plot/pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = [ "memilio", "memilio.plot", "memilio.plot_test"]
+
+[project]
+name = "memilio-plot"
+version = "1.0.0"
+readme = "README.md"
+authors = [{name = "DLR-SC", email = "[email protected]"}]
+maintainers = [{email = "[email protected]"}]
+description = "Part of MEmilio project, plots data to maps or visualizes simulation curves."
+requires-python = ">=3.8"
+dependencies = [
+    # smaller pandas versions contain a bug that sometimes prevents reading
+    # some excel files (e.g. population or twitter data)
+    "pandas>=1.2.2",
+    "matplotlib",
+    "tables",
+    # smaller numpy versions cause a security issue, 1.25 breaks testing with pyfakefs
+    "numpy>=1.22,<1.25",
+    "openpyxl",
+    "xlrd",
+    "requests",
+    "pyxlsb",
+    "wget",
+    "folium",
+    "mapclassify",
+    "geopandas",
+    "h5py",
+    "imageio",
+    "datetime"
+]
+
+[project.optional-dependencies]
+dev = [
+            # first support of python 3.11 4.6
+            # 5.3.4 has conflicts with openpyxl
+            # 5.3.3 broken
+            "pyfakefs>=4.6,<5.3.3",
+            # coverage 7.0.0 can't find .whl files and breaks CI
+            "coverage>=7.0.1",
+            # pylint 2.16 creates problem with wrapt package version
+            "pylint>=2.13.0,<2.16",
+            "pylint_json2html==0.4.0",
+        ]
+
+[project.urls] 
+Repository = "https://github.com/SciCompMod/memilio"
+Issues = "https://github.com/SciCompMod/memilio/issues"
+
+[project.scripts]
+memiliopylint = "memilio.custom_pylint:main"