Merge branch 'develop' of https://github.com/rkingsbury/pyEQL into de…

…velop
KingsburyLab · Aug 1, 2023 · 781ad4a · 781ad4a
2 parents c7155ed + 426d5c9
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,29 @@
+## Summary
+
+Major changes:
+
+- feature 1: ...
+- fix 1: ...
+
+## Todos
+
+If this is work in progress, what else needs to be done?
+
+- feature 2: ...
+- fix 2:
+
+## Checklist
+
+- [ ] Google format doc strings added.
+- [ ] Code linted with `ruff`. (For guidance in fixing rule violates, see [rule list](https://beta.ruff.rs/docs/rules/))
+- [ ] Type annotations included. Check with `mypy`.
+- [ ] Tests added for new features/fixes.
+- [ ] I have run the tests locally and they passed.
+<!-- - [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172)) -->
+
+Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
+
+```sh
+pip install -U pre-commit
+pre-commit install
+```
diff --git a/.github/workflows/post-process.yml b/.github/workflows/post-process.yml
@@ -0,0 +1,26 @@
+name: Post-process
+
+on:
+  workflow_run:
+    types:
+      - completed
+    workflows:
+      # List all required workflow names here.
+      - 'testing'
+
+jobs:
+# https://github.com/marketplace/actions/tag-release-on-push-action
+  auto-gen-release:
+    name: Tag/Release on merge of labeled PRs
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - # It is often a desired behavior to merge only when a workflow execution
+        # succeeds. This can be changed as needed.
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        uses: rymndhng/[email protected]
+        with:
+          # loonly release when PRs with release:major/minor/patch labels are merged
+          bump_version_scheme: norelease
+          use_github_release_notes: true
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,34 @@
+name: release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  # https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
+
+  deploy:
+    runs-on: ubuntu-latest
+    environment: publish
+
+    steps:
+    - uses: actions/checkout@v3
+
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools setuptools_scm wheel tox
+
+    - name: Build packages for distribution
+      run: |
+        tox -e build
+
+    - name: Upload to PyPi
+      uses: pypa/[email protected]
+      permissions:
+        id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -5,26 +5,28 @@ on: [push, pull_request]
 jobs:
   lint:
     runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
     steps:
       - uses: actions/checkout@v3
-      - name: Setup Python
+        with:
+          fetch-depth: 0
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
-      - name: Install tox
+          python-version: 3.11
+          cache: pip
+      - name: Run pre-commit
         run: |
-          python -m pip install tox
-      - name: Lint
-        run: tox -e lint
+          pip install pre-commit
+          pre-commit run
 
   test:
+    needs: lint
     strategy:
+      max-parallel: 6
       matrix:
-        python:
-        - "3.8"
-        - "3.9"
-        - "3.10"
-        # - "3.11"
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         platform:
         - ubuntu-latest
         - macos-latest

diff --git a/.github/workflows/upgrade_dependencies.yml b/.github/workflows/upgrade_dependencies.yml
@@ -0,0 +1,89 @@
+# https://www.oddbird.net/2022/06/01/dependabot-single-pull-request/
+# https://github.com/materialsproject/MPContribs/blob/master/.github/workflows/upgrade-dependencies.yml
+name: upgrade dependencies
+
+on:
+  workflow_dispatch: # Allow running on-demand
+  schedule:
+    # Runs every Monday at 8:00 UTC (4:00 Eastern)
+    - cron: '0 8 * * 1'
+
+jobs:
+  upgrade:
+    name: ${{ matrix.package }} (${{ matrix.os }}/py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        package: ["."]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Upgrade Python dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip pip-tools
+          cd ${{ matrix.package }}
+          python -m piptools compile -q --upgrade --resolver=backtracking -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}.txt
+          python -m piptools compile -q --upgrade --resolver=backtracking --all-extras -o requirements/${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
+      - name: Detect changes
+        id: changes
+        shell: bash
+        run: |
+          #git diff-index HEAD ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}*.txt | awk '{print $4}' | sort -u
+          #sha1=$(git diff-index HEAD ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}*.txt | awk '{print $4}' | sort -u | head -n1)
+          #[[ $sha1 == "0000000000000000000000000000000000000000" ]] && git update-index --really-refresh ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}*.txt
+          echo "count=$(git diff-index HEAD ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}*.txt | wc -l | xargs)" >> $GITHUB_OUTPUT
+          echo "files=$(git ls-files --exclude-standard --others ${{ matrix.package }}/requirements/${{ matrix.os }}_py${{ matrix.python-version }}*.txt | wc -l | xargs)" >> $GITHUB_OUTPUT
+      - name: commit & push changes
+        if: steps.changes.outputs.count > 0 || steps.changes.outputs.files > 0
+        shell: bash
+        run: |
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add ${{ matrix.package }}/requirements
+          git commit -m "update dependencies for ${{ matrix.package }} (${{ matrix.os }}/py${{ matrix.python-version }})"
+          git push -f origin ${{ github.ref_name }}:auto-dependency-upgrades-${{ matrix.package }}-${{ matrix.os }}-py${{ matrix.python-version }}
+
+  pull_request:
+    name: Merge all branches and open PR
+    runs-on: ubuntu-latest
+    needs: upgrade
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: detect auto-upgrade-dependency branches
+        id: changes
+        run: echo "count=$(git branch -r | grep auto-dependency-upgrades- | wc -l | xargs)" >> $GITHUB_OUTPUT
+      - name: merge all auto-dependency-upgrades branches
+        if: steps.changes.outputs.count > 0
+        run: |
+          git config user.name github-actions
+          git config user.email [email protected]
+          git checkout -b auto-dependency-upgrades
+          git branch -r | grep auto-dependency-upgrades- | xargs -I {} git merge {}
+          git rebase ${GITHUB_REF##*/}
+          git push -f origin auto-dependency-upgrades
+          git branch -r | grep auto-dependency-upgrades- | cut -d/ -f2 | xargs -I {} git push origin :{}
+      - name: Open pull request if needed
+        if: steps.changes.outputs.count > 0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        # Only open a PR if the branch is not attached to an existing one
+        run: |
+          PR=$(gh pr list --head auto-dependency-upgrades --json number -q '.[0].number')
+          if [ -z $PR ]; then
+            gh pr create \
+            --head auto-dependency-upgrades \
+            --title "Automated dependency upgrades" \
+            --body "Full log: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"
+          else
+            echo "Pull request already exists, won't create a new one."
+          fi
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,69 +1,42 @@
 exclude: '^docs/conf.py'
 
-repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
-  hooks:
-  - id: trailing-whitespace
-    args: [--markdown-linebreak-ext=md]
-    exclude_types: [tsv]
-  - id: check-added-large-files
-  - id: check-ast
-  - id: check-json
-  - id: check-merge-conflict
-  - id: check-xml
-  - id: check-yaml
-  - id: debug-statements
-  - id: end-of-file-fixer
-  - id: requirements-txt-fixer
-  - id: mixed-line-ending
-    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
-
-## If you want to avoid flake8 errors due to unused vars or imports:
-# - repo: https://github.com/myint/autoflake
-#   rev: v1.4
-#   hooks:
-#   - id: autoflake
-#     args: [
-#       --in-place,
-#       --remove-all-unused-imports,
-#       --remove-unused-variables,
-#     ]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.10.1
-  hooks:
-  - id: isort
-    args: ["--profile", "black", "--filter-files"]
+default_stages: [commit]
 
-- repo: https://github.com/psf/black
-  rev: 22.3.0
-  hooks:
-  - id: black
-    language_version: python3
+default_install_hook_types: [pre-commit, commit-msg]
 
-## If like to embrace black styles even in the docs:
-# - repo: https://github.com/asottile/blacken-docs
-#   rev: v1.12.0
-#   hooks:
-#   - id: blacken-docs
-#     additional_dependencies: [black]
+ci:
+  autoupdate_schedule: monthly
+  # skip: [mypy]
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 4.0.1
-  hooks:
-  - id: flake8
-  ## You can add flake8 plugins via `additional_dependencies`:
-  #  additional_dependencies: [flake8-bugbear]
-
-  ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit.com hooks
-
-        for more information, see https://pre-commit.ci
-    autofix_prs: true
-    autoupdate_branch: ''
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: weekly
-    skip: []
-    submodules: false
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.280
+    hooks:
+      - id: ruff
+        args: [--fix, --ignore, "D,E501"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+        exclude: ".tsv"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,7 +19,7 @@
 - Add more comprehensive platform testing via `tox`
 - Replace `water_properties.py` with [iapws](https://github.com/jjgomera/iapws) package
 - Replace elements.py with `pymatgen.core.periodic_table`
-- Add `pymatgen` as a depedency
+- Add `pymatgen` as a dependency
 - Migrate all tests to `pytest`
 - Add pre-commit configuration and lint with `black`
 - Update packaging to use [pyscaffold](https://pyscaffold.org/en/stable/index.html)

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ pyEQL is a Python library that provides tools for modeling aqueous electrolyte
 solutions. It allows the user to manipulate solutions as Python
 objects, providing methods to populate them with solutes, calculate
 species-specific properties (such as activity and diffusion coefficients),
-and retreive bulk properties (such as density, conductivity, or volume).
+and retrieve bulk properties (such as density, conductivity, or volume).
 
 ![pyeql demo](pyeql-demo.png)
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -8,8 +8,8 @@
 # serve to show the default.
 
 import os
-import sys
 import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
@@ -52,7 +52,7 @@
 
     apidoc.main(args)
 except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
+    print(f"Running `sphinx-apidoc` failed!\n{e}")
 
 # -- General configuration ---------------------------------------------------
 
@@ -114,7 +114,7 @@
 #
 # version: The short X.Y version.
 # release: The full version, including alpha/beta/rc tags.
-# If you don’t need the separation provided between version and release,
+# If you don`t need the separation provided between version and release,
 # just set them both to the same value.
 try:
     from pyEQL import __version__ as version
@@ -301,4 +301,4 @@
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
 
-print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
diff --git a/docs/database.rst b/docs/database.rst
@@ -19,7 +19,7 @@ following parameters for some common electrolytes:
 Basics
 ======
 
-The Paramsdb class creates a container for parameters. Each paramter
+The Paramsdb class creates a container for parameters. Each parameter
 is an object which contains not only the value, but also information about
 the units, the reference, and the conditions of measurement. paramsdb() also
 defines several methods that are helpful for retrieving parameters.

diff --git a/docs/index.md b/docs/index.md
@@ -7,7 +7,7 @@ Add a short description here!
 
 > This is the main page of your project's [Sphinx] documentation. It is
 > formatted in [Markdown]. Add additional pages by creating md-files in
-> `docs` or rst-files (formated in [reStructuredText]) and adding links to
+> `docs` or rst-files (formatted in [reStructuredText]) and adding links to
 > them in the `Contents` section below.
 >
 > Please check [Sphinx], [recommonmark] and [autostructify] for more information