Use pyproject.toml for project metadata, add citation info (MODFLOW-ORG#11)

mwtoews · web-flow · commit 61ccbb6687e1 · 2023-03-29T09:02:19.000-05:00
diff --git a/.flake8 b/.flake8
@@ -8,29 +8,24 @@ exclude =
     autotest
 ignore =
     # https://flake8.pycqa.org/en/latest/user/error-codes.html
-    F401, # 'module' imported but unused
+    # 'module' imported but unused
+    F401,
     # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
-    E121, # continuation line under-indented for hanging indent
-    E122, # continuation line missing indentation or outdented
-    E126, # continuation line over-indented for hanging indent
-    E127, # continuation line over-indented for visual indent
-    E128, # continuation line under-indented for visual indent
-    E203, # whitespace before
-    E221, # multiple spaces before operator
-    E222, # multiple spaces after operator
-    E226, # missing whitespace around arithmetic operator
-    E231, # missing whitespace after ','
-    E241, # multiple spaces after ','
-    E402, # module level import not at top of file
-    E501, # line too long (> 79 characters)
-    E502, # backslash is redundant between brackets
-    E722, # do not use bare 'except'
-    E741, # ambiguous variable name
-    W291, # trailing whitespace
-    W292, # no newline at end of file
-    W293, # blank line contains whitespace
-    W391, # blank line at end of file
-    W503, # line break before binary operator
-    W504  # line break after binary operator
+    # E1: Indentation
+    E121, E122, E126, E127, E128,
+    # E2: Whitespace
+    E203, E221, E222, E226, E231, E241,
+    # E4: Import
+    E402,
+    # E5: Line length
+    E501, E502,
+    # E7: Statement
+    E722, E741,
+    # W2: Whitespace warning
+    W291, W292, W293,
+    # W3: Blank line warning
+    W391,
+    # W5: Line break warning
+    W503, W504
 
 statistics = True
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v3
 
-    - name: Setup Python 3.8
+    - name: Setup Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.x
 
     - name: Upgrade pip
       run: |
@@ -64,29 +64,26 @@ jobs:
     # Standard python fails on Windows without GDAL installation. Using
     # standard python here since only linting on linux.
     # Use standard bash shell with standard python
-    - name: Setup Python 3.8
+    - name: Setup Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
-        cache: 'pip'
-        cache-dependency-path: setup.cfg
+        python-version: 3.x
 
     - name: Print python version
       run: |
         python --version
 
-    - name: Install Python dependencies
+    - name: Install Python packages
       run: |
         python -m pip install --upgrade pip
-        pip install .
-        pip install ".[lint]"
+        pip install -e .[lint]
 
     - name: Run black
       run: |
         echo "if black check fails run"
-        echo "  black --line-length 79 ./modflowapi"
+        echo "  black ./modflowapi"
         echo "and then commit the changes."
-        black --check --line-length 79 ./modflowapi
+        black --check ./modflowapi
 
     - name: Run flake8
       run: |
@@ -104,7 +101,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.8, 3.9, "3.10"]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
     defaults:
       run:
         shell: bash
@@ -119,21 +116,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-          cache-dependency-path: setup.cfg
+          cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
-        if: runner.os != 'Windows'
         run: |
           pip install --upgrade pip
-          pip install .
-          pip install ".[test]"
-
-      - name: Install Python dependencies Windows
-        if: runner.os == 'Windows'
-        run: |
-          python.exe -m pip install --upgrade pip
-          python.exe -m pip install .
-          python.exe -m pip install ".[test]"
+          pip install git+https://git@github.com/Deltares/xmipy@develop
+          pip install git+https://git@github.com/MODFLOW-USGS/modflow-devtools@develop
+          pip install .[test]
 
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
@@ -156,7 +146,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.8, 3.9, "3.10"]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
     defaults:
       run:
         shell: bash
@@ -171,21 +161,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-          cache-dependency-path: setup.cfg
+          cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
-        if: runner.os != 'Windows'
         run: |
           pip install --upgrade pip
-          pip install .
-          pip install ".[test]"
-
-      - name: Install Python dependencies Windows
-        if: runner.os == 'Windows'
-        run: |
-          python.exe -m pip install --upgrade pip
-          python.exe -m pip install .
-          python.exe -m pip install ".[test]"
+          pip install git+https://git@github.com/Deltares/xmipy@develop
+          pip install git+https://git@github.com/MODFLOW-USGS/modflow-devtools@develop
+          pip install .[test]
 
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
@@ -198,4 +181,4 @@ jobs:
         shell: bash -l {0}
         run: |
           # chmod a+x libmf6*
-          pytest -n auto -m "mf6 and not extensions"
+          pytest -n auto -m "mf6 and not extensions"
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,61 @@
+cff-version: 1.2.0
+message: If you use this software, please cite both the article from preferred-citation
+  and the software itself.
+type: software
+title: MODFLOW API
+version: 0.0.1
+date-released: '2021-05-12'
+abstract: An extension to xmipy for the MODFLOW API.
+repository-artifact: https://pypi.org/project/modflowapi
+repository-code: https://github.com/MODFLOW-USGS/modflowapi
+license: CC0-1.0
+authors:
+- family-names: Hughes
+  given-names: Joseph D.
+  alias: jdhughes-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0003-1311-2354
+- family-names: Russcher
+  given-names: Martijn
+  alias: mjr-deltares
+  affiliation: Deltares
+  orcid: https://orcid.org/0000-0001-8799-6514
+- family-names: Langevin
+  given-names: Christian D.
+  alias: langevin-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0001-5610-9759
+- family-names: Hofer
+  given-names: Julian
+  alias: Hofer-Julian
+  affiliation: Deltares
+- family-names: Larsen
+  given-names: Joshua D.
+  alias: jlarsen-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0002-1218-800X
+preferred-citation:
+  type: article
+  authors:
+  - family-names: Hughes
+    given-names: Joseph D.
+    orcid: https://orcid.org/0000-0003-1311-2354
+  - family-names: Russcher
+    given-names: Martijn J.
+    orcid: https://orcid.org/0000-0001-8799-6514
+  - family-names: Langevin
+    given-names: Christian D.
+    orcid: https://orcid.org/0000-0001-5610-9759
+  - family-names: Morway
+    given-names: Eric D.
+    orcid: https://orcid.org/0000-0002-8553-6140
+  - family-names: McDonald
+    given-names: Richard R.
+    orcid: https://orcid.org/0000-0002-0703-0638
+  title: The MODFLOW Application Programming Interface for simulation control and software interoperability
+  doi: 10.1016/j.envsoft.2021.105257
+  journal: Environmental Modelling & Software
+  volume: 138
+  start: 105257
+  year: 2022
+  month: 2
diff --git a/README.md b/README.md
@@ -9,3 +9,7 @@ and additional functionality specific to the MODFLOW API. Currently it is a join
 ```
 pip install modflowapi
 ```
+
+### Citation
+
+Hughes, Joseph D., Russcher, M. J., Langevin, C. D., Morway, E. D. and McDonald, R. R., 2022, The MODFLOW Application Programming Interface for simulationcontrol and software interoperability: Environmental Modelling & Software, v. 148, p. 105257, [doi:10.1016/j.envsoft.2021.105257](https://doi.org/10.1016/j.envsoft.2021.105257).
diff --git a/etc/requirements.pip.txt b/etc/requirements.pip.txt
diff --git a/guide-to-publish.md b/guide-to-publish.md
@@ -2,17 +2,17 @@
 
 1) If present delete dist folder
 
-2) If not done yet, install twine via
+2) If not done yet, install build and twine via
 ```
-pip install twine
+pip install build twine
 ```
-3) Update the version number in the setup.py file.
+3) Update the version in ``modflowapi/version.py``
 
 4) Re-create the wheels:
 ```
-python setup.py sdist bdist_wheel
+python -m build
 ```
 5) Re-upload the new files:
 ```
 twine upload dist/*
-```
+```
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools >=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "modflowapi"
+dynamic = ["version"]
+authors = [
+    {name = "Joseph D. Hughes", email = "jdhughes@usgs.gov"},
+    {name = "Martijn Russcher", email = "Martijn.Russcher@deltares.nl"},
+    {name = "Christian D. Langevin", email = "langevin@usgs.gov"},
+    {name = "Julian Hofer", email = "Julian.Hofer@deltares.nl"},
+    {name = "Joshua D. Larsen", email = "jlarsen@usgs.gov"},
+]
+maintainers = [
+    {name = "Joseph D. Hughes", email = "jdhughes@usgs.gov"},
+]
+description = "modflowapi is an extension to the xmipy Python package"
+readme = "README.md"
+keywords = ["MODFLOW", "groundwater", "hydrogeology", "bmi", "xmi"]
+license = {text = "CC0"}
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Hydrology",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "pandas",
+    "xmipy",  # develop branch from github.com/Deltares/xmipy
+]
+
+[project.optional-dependencies]
+dev = ["modflowapi[test,lint]"]
+test = [
+    "filelock",
+    "modflow-devtools",  # develop branch from github.com/MODFLOW-USGS/modflow-devtools
+    "pytest",
+    "pytest-order",
+    "pytest-xdist",
+]
+lint = [
+    "black",
+    "flake8",
+    "pylint",
+]
+
+[project.urls]
+Repository = "https://github.com/MODFLOW-USGS/modflowapi"
+Publication = "https://doi.org/10.1016/j.envsoft.2021.105257"
+
+[tool.setuptools.dynamic]
+version = {attr = "modflowapi.version.__version__"}
+
+[tool.setuptools.packages.find]
+include = ["modflowapi", "modflowapi.*"]
+
+[tool.black]
+line-length = 79
+target_version = ["py37"]
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
