openpathsampling · dwhswenson · Nov 28, 2020 · Sep 26, 2020 · Sep 26, 2020 · Sep 26, 2020
diff --git a/.github/workflows/autorelease-default-env.sh b/.github/workflows/autorelease-default-env.sh
@@ -0,0 +1,5 @@
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3"
+if [ -f autorelease-env.sh ]; then
+    source autorelease-env.sh
+fi
+
diff --git a/.github/workflows/autorelease-deploy.yml b/.github/workflows/autorelease-deploy.yml
@@ -0,0 +1,31 @@
+name: Autorelease
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy_pypi:
+    runs-on: ubuntu-latest
+    name: "Deploy to PyPI"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          cat autorelease-env.sh >> $GITHUB_ENV
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          python -m pip install twine wheel
+        name: "Install release tools"
+      - run: |
+          python setup.py sdist bdist_wheel
+          twine check dist/*
+        name: "Build and check package"
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_password }}
+        name: "Deploy to testpypi"
+
diff --git a/.github/workflows/autorelease-gh-rel.yml b/.github/workflows/autorelease-gh-rel.yml
@@ -0,0 +1,27 @@
+name: Autorelease
+on:
+  push:
+    branches:
+      - stable
+
+jobs:
+  release-gh:
+    runs-on: ubuntu-latest
+    name: "Cut release"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          cat autorelease-env.sh >> $GITHUB_ENV
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          VERSION=`python setup.py --version`
+          PROJECT=`python setup.py --name`
+          echo $PROJECT $VERSION
+          autorelease-release --project $PROJECT --version $VERSION --token $AUTORELEASE_TOKEN
+        env:
+          AUTORELEASE_TOKEN: ${{ secrets.AUTORELEASE_TOKEN }}
diff --git a/.github/workflows/autorelease-prep.yml b/.github/workflows/autorelease-prep.yml
@@ -0,0 +1,56 @@
+name: "Autorelease"
+on:
+  pull_request:
+    branches:
+      - stable
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  deploy_testpypi:
+    runs-on: ubuntu-latest
+    name: "Deployment test"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          cat autorelease-env.sh >> $GITHUB_ENV
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: |
+          python -m pip install twine wheel
+        name: "Install release tools"
+      - run: |
+          bump-dev-version
+          python setup.py --version
+        name: "Bump testpypi dev version"
+      - run: |
+          python setup.py sdist bdist_wheel
+          twine check dist/*
+        name: "Build and check package"
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.testpypi_password }}
+          repository_url: https://test.pypi.org/legacy/
+        name: "Deploy to testpypi"
+  test_testpypi:
+    runs-on: ubuntu-latest
+    name: "Test deployed"
+    needs: deploy_testpypi
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - run: |  # TODO: move this to an action
+          source ./.github/workflows/autorelease-default-env.sh
+          cat autorelease-env.sh >> $GITHUB_ENV
+          eval $INSTALL_AUTORELEASE
+        name: "Install autorelease"
+      - run: test-testpypi
+
diff --git a/.github/workflows/test-suite.yml b/.github/workflows/test-suite.yml
@@ -0,0 +1,64 @@
+name: "Tests"
+
+on:
+  pull_request:
+    branches:
+      - master
+      - stable
+  push:
+    branches:
+      - master
+    tags:
+      - "v*"
+  schedule:
+    - cron: "25 5 * * *"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  test_suite:
+    runs-on: ubuntu-latest
+    name: "Unit tests"
+    strategy:
+      matrix:
+        CONDA_PY:
+          - 3.9
+          - 3.8
+          - 3.7
+          - 3.6
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.CONDA_PY }}
+      - name: "Install testing tools"
+        run: python -m pip install -r ./devtools/tests_require.txt
+      - name: "Install"
+        run: |
+          conda install pip
+          python -m pip install -e .
+      - name: "Versions"
+        run: conda list
+      - name: "Autorelease check"
+        env:
+          PR_BRANCH: ${{ github.event.pull_request.base.ref }}
+          REF: ${{ github.ref }}
+          EVENT: ${{ github.event_name }}
+        run: |
+          if [ "$EVENT" != "pull_request" ]; then
+            BRANCH=$REF
+          else
+            BRANCH=$PR_BRANCH
+          fi
+          python autorelease_check.py --branch $BRANCH --even ${EVENT}
+      - name: "Unit tests"
+        run: |
+          python -c "import paths_cli"
+          py.test -vv --cov --cov-report xml:cov.xml
+      - name: "Report coverage"
+        run: bash <(curl -s https://codecov.io/bash)
diff --git a/.travis.yml b/.travis.yml
diff --git a/autorelease-env.sh b/autorelease-env.sh
@@ -0,0 +1,2 @@
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3 nose"
+PACKAGE_IMPORT_NAME=paths_cli
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -0,0 +1,67 @@
+.. _api:
+
+API
+===
+
+.. currentmodule:: paths_cli
+
+CLI and Plugins
+---------------
+
+.. autosummary::
+    :toctree: generated
+
+    OpenPathSamplingCLI
+    plugin_management.CLIPluginLoader
+    plugin_management.FilePluginLoader
+    plugin_management.NamespacePluginLoader
+
+
+Parameter Decorators
+--------------------
+
+These are the functions used to create the reusable parameter decorators.
+Note that you will probably never need to use these; instead, use the
+existing parameter decorators.
+
+.. autosummary::
+    :toctree: generated
+
+    param_core.Option
+    param_core.Argument
+    param_core.AbstractLoader
+    param_core.StorageLoader
+    param_core.OPSStorageLoadNames
+    param_core.OPSStorageLoadSingle
+
+Search strategies
+-----------------
+
+These are the various strategies for finding objects in a storage, in
+particular if we have to guess because the user didn't provide an explicit
+choice or didn't tag.
+
+.. autosummary::
+    :toctree: generated
+
+    param_core.Getter
+    param_core.GetByName
+    param_core.GetByNumber
+    param_core.GetPredefinedName
+    param_core.GetOnly
+    param_core.GetOnlyNamed
+    param_core.GetOnlySnapshot
+
+
+Commands
+--------
+
+.. autosummary::
+    :toctree: generated
+    :recursive:
+
+    commands.visit_all
+    commands.equilibrate
+    commands.pathsampling
+    commands.append
+    commands.contents
diff --git a/docs/conf.py b/docs/conf.py
@@ -41,9 +41,13 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     'sphinx_click.ext',
 ]
 
+autosummary_generate = True
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

diff --git a/docs/for_core/README.md b/docs/for_core/README.md
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.3 nose"
		PACKAGE_IMPORT_NAME=paths_cli