pyStrata 0.5.3__tar.gz → 0.6.0__tar.gz

pystrata-0.6.0/.coveragerc

@@ -0,0 +1,10 @@
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError
+    if __name__ == .__main__.:

pystrata-0.6.0/.editorconfig

@@ -0,0 +1,22 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+max_line_length = 79
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

pystrata-0.6.0/.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# Migrated code style to Black
+d26b8a65f11020d4574f6c408963922d7b5de1f5
+# Migrated code style to Black
+3c0ccfd90a41bd557d2254783eed150c31a81cf2

pystrata-0.6.0/.github/dependabot.yml

@@ -0,0 +1,33 @@
+version: 2
+
+updates:
+    # Python dependencies, resolved through uv.lock.
+    #
+    # Security updates are enabled separately in the repository settings and
+    # only cover direct dependencies with a known advisory. Most of this
+    # project's alerts are against transitive packages pinned in uv.lock
+    # (mistune and bleach via nbconvert, starlette and tornado via the docs
+    # server, pillow via matplotlib), which are only bumped when the lock file
+    # itself is refreshed -- that is what these version updates do.
+    - package-ecosystem: "uv"
+      directory: "/"
+      schedule:
+          interval: "weekly"
+          day: "sunday"
+      open-pull-requests-limit: 10
+      commit-message:
+          prefix: "deps"
+      groups:
+          # One pull request per week for the routine bumps, rather than one
+          # per package. Majors stay ungrouped so they are reviewed on their
+          # own.
+          production:
+              dependency-type: "production"
+              update-types:
+                  - "minor"
+                  - "patch"
+          development:
+              dependency-type: "development"
+              update-types:
+                  - "minor"
+                  - "patch"

pystrata-0.6.0/.github/workflows/dependabot-auto-merge.yml

@@ -0,0 +1,70 @@
+# Merges Dependabot's grouped development-dependency updates once every check
+# on the pull request has passed. Production dependencies and major bumps are
+# left for manual review, so nothing that ships to users merges unreviewed.
+#
+# The CI gate is implemented here rather than through branch protection with
+# required status checks, because that would also refuse direct pushes to the
+# branch until checks pass.
+
+name: Dependabot auto-merge
+
+# Both workflows run on a pull request. Triggering on either means whichever
+# finishes last sees a fully green commit; the earlier one finds the other
+# still running and does nothing.
+on:
+    workflow_run:
+        workflows: ["Python application", "Lint with Ruff"]
+        types: [completed]
+
+permissions:
+    contents: write
+    pull-requests: write
+
+jobs:
+    auto-merge:
+        runs-on: ubuntu-latest
+        if: >
+            github.event.workflow_run.conclusion == 'success' &&
+            github.event.workflow_run.event == 'pull_request' &&
+            github.event.workflow_run.actor.login == 'dependabot[bot]'
+
+        steps:
+            - name: Merge when every check has passed
+              env:
+                  GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                  REPO: ${{ github.repository }}
+                  SHA: ${{ github.event.workflow_run.head_sha }}
+                  BRANCH: ${{ github.event.workflow_run.head_branch }}
+              run: |
+                  set -euo pipefail
+
+                  # Only the grouped development updates merge on their own. The
+                  # group name is defined in .github/dependabot.yml and appears
+                  # in the branch Dependabot creates.
+                  case "$BRANCH" in
+                      dependabot/*/development-*) ;;
+                      *)
+                          echo "Branch $BRANCH is not the development group; leaving for review."
+                          exit 0
+                          ;;
+                  esac
+
+                  pr=$(gh api "repos/$REPO/commits/$SHA/pulls" --jq '.[0].number // empty')
+                  if [ -z "$pr" ]; then
+                      echo "No pull request found for $SHA."
+                      exit 0
+                  fi
+
+                  # One workflow finishing does not mean the commit is green.
+                  unfinished=$(gh api "repos/$REPO/commits/$SHA/check-runs" --paginate \
+                      --jq '[.check_runs[]
+                             | select(.status != "completed"
+                                      or (.conclusion | IN("success", "skipped", "neutral") | not))]
+                            | length')
+                  if [ "$unfinished" -ne 0 ]; then
+                      echo "$unfinished check(s) still running or not successful; not merging."
+                      exit 0
+                  fi
+
+                  echo "All checks passed; merging #$pr."
+                  gh pr merge "$pr" --repo "$REPO" --squash --delete-branch

pystrata-0.6.0/.github/workflows/docs.yml

@@ -0,0 +1,19 @@
+name: Build docs
+
+on: [push, pull_request]
+
+jobs:
+    docs:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7.0.1
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            # nbsphinx converts the notebooks with pandoc
+            - name: Install pandoc
+              run: sudo apt-get update && sudo apt-get install -y pandoc
+            # Warnings are errors, so that broken references and markup are caught
+            - name: Build the documentation
+              run: uv run --extra docs sphinx-build -b html -W --keep-going docs docs/_build/html

pystrata-0.6.0/.github/workflows/interop.yml

@@ -0,0 +1,63 @@
+name: Interop
+
+# Test this package against the development branches of its siblings. They
+# depend on each other (pystrata on pyrvt, pygmm on pyrotd, and their tests on
+# each other), and the locked releases on PyPI lag the development branches.
+on: [push, pull_request]
+
+jobs:
+    interop:
+        runs-on: ubuntu-latest
+        steps:
+            - name: Check out this repository
+              uses: actions/checkout@v7.0.1
+              with:
+                  path: ${{ github.event.repository.name }}
+                  fetch-depth: 0
+            - name: Check out pystrata (development branch)
+              if: github.event.repository.name != 'pystrata'
+              uses: actions/checkout@v7.0.1
+              with:
+                  repository: arkottke/pystrata
+                  ref: dev
+                  path: pystrata
+                  fetch-depth: 0
+            - name: Check out pygmm (development branch)
+              if: github.event.repository.name != 'pygmm'
+              uses: actions/checkout@v7.0.1
+              with:
+                  repository: arkottke/pygmm
+                  ref: dev
+                  path: pygmm
+                  fetch-depth: 0
+            - name: Check out pyrvt (development branch)
+              if: github.event.repository.name != 'pyrvt'
+              uses: actions/checkout@v7.0.1
+              with:
+                  repository: arkottke/pyrvt
+                  ref: dev
+                  path: pyrvt
+                  fetch-depth: 0
+            - name: Check out pyrotd (development branch)
+              if: github.event.repository.name != 'pyrotd'
+              uses: actions/checkout@v7.0.1
+              with:
+                  repository: arkottke/pyrotd
+                  ref: dev
+                  path: pyrotd
+                  fetch-depth: 0
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            - name: Install the four packages from source
+              run: |
+                  uv venv --python 3.13 .venv
+                  uv pip install --python .venv/bin/python \
+                    -e "./pyrvt[cli,test]" -e "./pygmm[slope,test]" \
+                    -e "./pystrata[test]" -e ./pyrotd pytest-cov
+            - name: Test
+              # The interop tests are skipped unless the siblings are installed
+              run: |
+                  cd ${{ github.event.repository.name }}
+                  ../.venv/bin/python -m pytest -ra

pystrata-0.6.0/.github/workflows/linter.yml

@@ -0,0 +1,17 @@
+name: Lint with Ruff
+on: [push, pull_request]
+jobs:
+    ruff:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7.0.1
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            - name: Set up Python
+              run: uv python install 3.13
+            - name: Install dependencies
+              run: uv sync --dev
+            - name: Run pre-commit on all files
+              run: uv run pre-commit run --all-files

pystrata-0.6.0/.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on: [push, pull_request]
+
+jobs:
+    pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7.0.1
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            # The same hooks as a local commit: formatting, whitespace and prettier
+            - name: Run pre-commit
+              run: uvx pre-commit run --all-files --show-diff-on-failure

pystrata-0.6.0/.github/workflows/python-app.yml

@@ -0,0 +1,39 @@
+name: Python application
+
+on: [push, pull_request]
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.13", "3.14"]
+
+        steps:
+            - uses: actions/checkout@v7.0.1
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            - name: Set up Python ${{ matrix.python-version }}
+              run: uv python install ${{ matrix.python-version }}
+            - name: Install dependencies
+              run: |
+                  uv sync --all-extras --dev
+            - name: Lint with ruff
+              run: |
+                  uv run ruff check .
+            - name: Format check with ruff
+              run: |
+                  uv run ruff format --check .
+            - name: Install package
+              run: |
+                  uv pip install -e .
+            - name: Test with pytest
+              run: |
+                  uv run pytest --cov-config=pyproject.toml --cov=pystrata --cov=tests --cov-report xml
+            - name: Run codacy-coverage-reporter
+              uses: codacy/codacy-coverage-reporter-action@v1.3.0
+              with:
+                  project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+                  coverage-reports: coverage.xml

pystrata-0.6.0/.github/workflows/python-publish.yml

@@ -0,0 +1,33 @@
+# Uploads the package to PyPI when a release is created.
+#
+# Authentication uses PyPI Trusted Publishing: GitHub mints a short-lived OIDC
+# token scoped to this workflow, so there is no long-lived API token stored as
+# a repository secret. The matching publisher is configured on PyPI under the
+# project's Publishing settings and must name this repository and this
+# workflow file.
+
+name: Upload Python Package
+
+on:
+    release:
+        types: [created]
+
+jobs:
+    deploy:
+        runs-on: ubuntu-latest
+
+        permissions:
+            contents: read
+            # Required to mint the OIDC token used for trusted publishing
+            id-token: write
+
+        steps:
+            - uses: actions/checkout@v7.0.1
+            - name: Install uv
+              uses: astral-sh/setup-uv@v9.0.0
+              with:
+                  version: "latest"
+            - name: Build
+              run: uv build
+            - name: Publish to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1

pystrata-0.6.0/.github/workflows/updater.yaml

@@ -0,0 +1,25 @@
+name: GitHub Actions Version Updater
+
+# Controls when the action will run.
+on:
+    workflow_dispatch:
+
+    schedule:
+        # Automatically run on every Sunday
+        - cron: "0 0 * * 0"
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v7.0.1
+              with:
+                  # [Required] Access token with `workflow` scope.
+                  token: ${{ secrets.UPDATER_TOKEN }}
+
+            - name: Run GitHub Actions Version Updater
+              uses: saadmk11/github-actions-version-updater@v0.9.0
+              with:
+                  # [Required] Access token with `workflow` scope.
+                  token: ${{ secrets.UPDATER_TOKEN }}

{pystrata-0.5.3 → pystrata-0.6.0}/.gitignore

@@ -19,6 +19,8 @@
 .idea/**/dynamic.xml
 .idea/**/uiDesigner.xml
 
+.vscode/
+
 # Gradle:
 .idea/**/gradle.xml
 .idea/**/libraries
@@ -122,6 +124,7 @@ target/
 
 # pyenv
 .python-version
+src/pystrata/_version.py
 
 # celery beat schedule file
 celerybeat-schedule
@@ -185,3 +188,8 @@ tags
 references/
 working/
 scratch.*
+
+.DS_Store
+
+# Local PyPI credentials file
+.pyirc

pystrata-0.6.0/.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+# Scientific data files are read with fixed-width or exact parsing, so the
+# whitespace and end-of-file hooks must not rewrite them.
+exclude: '^(data/|tests/data/|src/pystrata/data/|examples/data/)'
+repos:
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.15.4
+      hooks:
+                # Run the formatter.
+          - id: ruff-format
+            # Run the linter.
+          - id: ruff
+            args:
+                [--fix]
+    - repo: https://github.com/PyCQA/docformatter
+      rev: v1.7.7
+      hooks:
+          - id: docformatter
+            language_version: python3.12
+            args:
+                [--in-place, --wrap-summaries=88, --wrap-descriptions=88]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v6.0.0
+      hooks:
+          - id: trailing-whitespace
+          - id: check-json
+          # Unsafe required for mkdocs.yml format
+          - id: check-yaml
+            args: [--unsafe]
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: requirements-txt-fixer
+    - repo: local
+      hooks:
+          # Pinned: the pre-commit mirror only offers 4.0 alphas after 3.1.0, and
+          # 4.0.0-alpha.8 hangs. Needs node on PATH.
+          - id: prettier
+            name: prettier
+            entry: prettier --write --ignore-unknown
+            language: node
+            additional_dependencies: ["prettier@3.9.10"]
+            files: \.(md|yml)$

pystrata-0.6.0/.prettierignore

@@ -0,0 +1,8 @@
+# Generated or vendored
+_build/
+_autosummary/
+htmlcov/
+.venv/
+node_modules/
+*.egg-info/
+uv.lock

pystrata-0.6.0/.prettierrc

@@ -0,0 +1,4 @@
+{
+  "proseWrap": "preserve",
+  "endOfLine": "lf"
+}

pystrata-0.6.0/.readthedocs.yaml

@@ -0,0 +1,23 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    # The floor of requires-python; see "Version support policy" in CLAUDE.md
+    python: "3.13"
+  apt_packages:
+    # nbsphinx converts the markdown of the example notebooks with pandoc
+    - pandoc
+
+# The notebooks are not executed (nbsphinx_execute = "never" in docs/conf.py)
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs