shipgrav 1.0.4__tar.gz

shipgrav-1.0.4/.github/test_conda_env.yml

@@ -0,0 +1,12 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - numpy
+  - scipy
+  - pandas
+  - statsmodels
+  - tomli
+  - pyyaml
+  - coverage
+  - tqdm

shipgrav-1.0.4/.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [workflow_dispatch]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

shipgrav-1.0.4/.github/workflows/release-publish.yml

@@ -0,0 +1,119 @@
+name: Publish Python 🐍 distribution 📦 to TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to TestPyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/shipgrav
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/shipgrav
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

shipgrav-1.0.4/.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: tests
+on:
+  push:
+    branches:
+      - main
+  #workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron:  '42 0 * * 6'
+jobs:
+  run_tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: [3.9, "3.10","3.13"]
+        add_package: [""]
+        continue-on-error: [false]
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.continue-on-error }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python }}
+          environment-file: .github/test_conda_env.yml
+      - name: print conda environment info
+        run: |
+          conda info -a
+          conda list
+      - name: install package
+        run: |
+          pip install -v --no-deps .
+          conda list
+      - name: run test suite
+        run: |
+          mkdir empty; cd empty
+          cp -r ../shipgrav/tests/ex_files .
+          coverage run --include='*/shipgrav/*' -m shipgrav.tests
+          coverage xml -o ../coverage.xml
+      - name: upload coverage
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

shipgrav-1.0.4/.gitignore

@@ -0,0 +1,7 @@
+*.swp
+shipgrav/__pycache__/
+example-scripts/data*/
+shipgrav/tests/__pycache__/
+shipgrav/tests/.coverage
+docs/_build/
+*.code-workspace

shipgrav-1.0.4/.readthedocs.yml

@@ -0,0 +1,13 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

shipgrav-1.0.4/CHANGELOG

@@ -0,0 +1,50 @@
+2024-11-01  Hannah F Mark  <hmark@whoi.edu>
+
+    * update dependencies and docs
+    * add a flag to turn progress bars on/off so tests are cleaner
+    * add more tests for better coverage, fix bugs discovered by tests
+    * format example scripts for jupytext, update docs and optional dependencies
+    * update example scripts to use pooch for download, delete data_download script
+    * add progress bars for things (mostly file reads) and tqdm dependency
+
+2024-10-29  Hannah F Mark  <hmark@whoi.edu>
+
+    * clean/format code with isort and flake8
+    * update triggers for test workflow: run on push and on PR
+    * use abs path for example files so tests can be run from outside tests/ dir
+
+v1.0.3
+
+2024-10-25  Hannah F Mark  <hmark@whoi.edu>
+
+    * update pkg_resources (deprecated from 3.13) to importlib.resources for test suite
+    * fix download_data.sh curl by adding -L to follow R2R links
+    * fix SyntaxWarning for regular expressions in io.py by making raw strings
+    * fix DeprecationWarning for parse_dates with nested sequences, sub in pd.to_datetime
+    * fix FutureWarning for to_numeric, apply by column instead of whole DataFrame
+    * add geographiclib as dependency for RMBA example script (used for line extension)
+    * set tests to run on push (keeping scheduled ones too)
+    * add Python 3.13 to the test matrix, simplify the os matrix logic
+    * update codecov action to v4 for nodejs version
+    * update CONTRIBUTORS -> to markdown, with info on who did what prior to github upload
+    * fix indexing in one part of RMBA example script for future deprecation of chained assignment
+    * add detail to contributor guidelines
+
+v1.0.2
+
+2024-09-17  Hannah F Mark  <hmark@whoi.edu>
+
+    * update docs and optional dependencies
+
+v1.0.1
+
+2024-07-15  Hannah F Mark  <hmark@whoi.edu>
+
+    * PEP8 reformat, typos
+    * include some 2D functions for Parker method, rename the 1D one
+    * repo is now in PFPE org instead of WHOIGit
+
+2024-04-23  Hannah F Mark  <hmark@whoi.edu>
+
+    * docs/conf.py, readme.md, shipgrav/__init__.py: updated repo URLS
+    after repo tranfered to WHOIGit

shipgrav-1.0.4/CONTRIBUTORS.md

@@ -0,0 +1,27 @@
+# Contributors
+Contributors to shipgrav are listed and described using the [Contributor Role Taxonomoy (CRediT)](https://credit.niso.org/)
+
+## Hannah F. Mark
+- Conceptualization
+- Data curation
+- Software
+- Visualization
+- Writing -- original draft (JOSS)
+- Writing -- review and editing (JOSS)
+
+## Masako Tominaga
+- Conceptualization
+- Funding acquisition
+- Supervision
+- Validation
+- Writing -- review and editing (JOSS)
+
+## Jasmine Zhu
+- Software
+
+## Maurice Tivey
+- Funding acquisition
+- Writing -- review and editing (JOSS)
+
+## Daniel Aliod
+- Software