Improve infrastructure (CI, Linting, Docs Build)

.envs/testenv-linkcheck.yml

@@ -0,0 +1,22 @@
+name: estimagic
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - jupyterlab  # dev, docs
+  - nb_black  # dev, docs
+  - pip  # dev, tests, docs
+
+
+  - pydata-sphinx-theme>=0.3.0  # docs
+  - myst-parser  # docs
+  - nbsphinx  # docs
+  - sphinx  # docs
+  - sphinx-copybutton  # docs
+  - sphinx-panels  # docs
+  - sphinxcontrib-bibtex  # docs
+
+  - pip:  # dev, tests, docs
+    - -e ../

.envs/testenv-linux.yml

@@ -0,0 +1,37 @@
+name: estimagic
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - jax
+  - pygmo
+  - nlopt  # dev, tests
+  - pip  # dev, tests, docs
+  - pytest  # dev, tests
+  - pytest-cov  # tests
+  - pytest-xdist  # dev, tests
+  - statsmodels  # dev, tests
+
+  - bokeh<=2.4.3  # run, tests
+  - click  # run, tests
+  - cloudpickle  # run, tests
+  - fuzzywuzzy  # run, tests
+  - joblib  # run, tests
+  - numba  # run, tests
+  - numpy>=1.17.0  # run, tests
+  - pandas  # run, tests
+  - plotly  # run, tests
+  - pybaum >= 0.1.2  # run, tests
+  - scipy>=1.2.1  # run, tests
+  - sqlalchemy>=1.3  # run, tests
+
+
+  - pip:  # dev, tests, docs
+    - DFO-LS  # dev, tests
+    - Py-BOBYQA  # dev, tests
+    - fides==0.7.4  # dev, tests
+    - kaleido  # dev, tests
+    - simoptlib==1.0.1  # dev, tests
+    - -e ../

.envs/testenv-others.yml

@@ -0,0 +1,36 @@
+name: estimagic
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - cyipopt
+  - nlopt  # dev, tests
+  - pip  # dev, tests, docs
+  - pytest  # dev, tests
+  - pytest-cov  # tests
+  - pytest-xdist  # dev, tests
+  - statsmodels  # dev, tests
+
+  - bokeh<=2.4.3  # run, tests
+  - click  # run, tests
+  - cloudpickle  # run, tests
+  - fuzzywuzzy  # run, tests
+  - joblib  # run, tests
+  - numba  # run, tests
+  - numpy>=1.17.0  # run, tests
+  - pandas  # run, tests
+  - plotly  # run, tests
+  - pybaum >= 0.1.2  # run, tests
+  - scipy>=1.2.1  # run, tests
+  - sqlalchemy>=1.3  # run, tests
+
+
+  - pip:  # dev, tests, docs
+    - DFO-LS  # dev, tests
+    - Py-BOBYQA  # dev, tests
+    - fides==0.7.4  # dev, tests
+    - kaleido  # dev, tests
+    - simoptlib==1.0.1  # dev, tests
+    - -e ../

.envs/update_envs.py

@@ -0,0 +1,50 @@
+from copy import deepcopy
+from pathlib import Path
+
+
+def _keep_line(line: str, flag: str) -> bool:
+    """Return True if line contains flag and does not include a comment.
+
+    Examples:
+    >>> assert _keep_line("  - jax  # tests", "tests") is True
+    >>> assert _keep_line("name: env", "tests") is True
+    >>> assert _keep_line("  - jax  # run", "tests") is False
+    """
+    return flag in line or "#" not in line
+
+
+def main():
+
+    lines = Path("environment.yml").read_text().splitlines()
+
+    # create standard testing environments
+
+    test_env = [line for line in lines if _keep_line(line, "tests")]
+    test_env.append("    - -e ../")  # add local installation
+
+    # find index to insert additional dependencies
+    _insert_idx = [i for i, line in enumerate(lines) if "dependencies:" in line][0] + 1
+
+    ## linux
+    test_env_linux = deepcopy(test_env)
+    test_env_linux.insert(_insert_idx, "  - pygmo")
+    test_env_linux.insert(_insert_idx, "  - jax")
+
+    ## test environment others
+    test_env_others = deepcopy(test_env)
+    test_env_others.insert(_insert_idx, "  - cyipopt")
+
+    # create docs testing environment
+
+    docs_env = [line for line in lines if _keep_line(line, "docs")]
+    docs_env.append("    - -e ../")  # add local installation
+
+    # write environments
+    for name, env in zip(
+        ["linux", "others", "linkcheck"], [test_env_linux, test_env_others, docs_env]
+    ):
+        Path(f".envs/testenv-{name}.yml").write_text("\n".join(env) + "\n")
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/main.yml

@@ -5,6 +5,7 @@ concurrency:
   group: ${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
+
 on:
   push:
     branches:
@@ -13,6 +14,7 @@ on:
     branches:
     - '*'
 
+
 jobs:
 
   run-tests-linux:
@@ -27,27 +29,29 @@ jobs:
         python-version: ['3.8', '3.9', '3.10']
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - name: create build environment
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: conda install -c conda-forge tox-conda
-
-      - name: Run pytest.
+          environment-file: ./.envs/testenv-linux.yml
+          environment-name: estimagic
+          cache-env: true
+          extra-specs: |
+            python=${{ matrix.python-version }}
+      - name: run pytest
         shell: bash -l {0}
-        run: tox -e pytest-linux -- --cov-report=xml --cov=./
+        run: |
+          micromamba activate estimagic
+          pytest --cov-report=xml --cov=./
 
       - name: Upload coverage report.
         if: runner.os == 'Linux' && matrix.python-version == '3.10'
         uses: codecov/codecov-action@v1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
-  run-tests:
+
+  run-tests-win-and-mac:
 
     name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
@@ -59,57 +63,60 @@ jobs:
         python-version: ['3.8', '3.9', '3.10']
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - name: create build environment
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install core dependencies.
+          environment-file: ./.envs/testenv-others.yml
+          environment-name: estimagic
+          cache-env: true
+          extra-specs: |
+            python=${{ matrix.python-version }}
+      - name: run pytest
         shell: bash -l {0}
-        run: conda install -c conda-forge tox-conda
+        run: |
+          micromamba activate estimagic
+          pytest -m "not slow and not jax"
 
-      - name: Run pytest.
-        shell: bash -l {0}
-        run: tox -e pytest -- -m "not slow and not jax"
 
-  docs:
+  check-links-in-documentation:
 
-    name: Run documentation.
+    name: Check links in documentation.
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - name: create build environment
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          auto-update-conda: true
-          python-version: "3.10"
-
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: conda install -c conda-forge tox-conda
-
-      - name: Build docs
+          environment-file: ./.envs/testenv-linkcheck.yml
+          environment-name: estimagic
+          cache-env: true
+          extra-specs: python=3.10
+      - name: run sphinx
         shell: bash -l {0}
-        run: tox -e sphinx
-
+        run: |
+          micromamba activate estimagic
+          cd docs/source
+          sphinx-build -T -b linkcheck -d doctrees . linkcheck
 
   code-in-docs:
-
-    name: Run code snippets in documentation.
+    name: Run code snippets in documentation
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - name: create build environment
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          auto-update-conda: true
-          python-version: "3.10"
-
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: conda install -c conda-forge tox-conda
+          environment-file: ./.envs/testenv-linux.yml
+          environment-name: estimagic
+          cache-env: true
+          extra-specs: python=3.10
 
-      - name: Run doctest
+      - name: run sphinx
         shell: bash -l {0}
-        run: tox -e code-in-docs
+        run: |
+          micromamba activate estimagic
+          cd docs/source
+          python -m doctest -v how_to_guides/optimization/how_to_specify_constraints.md