Unverified Commit 53fc4d13 authored by Zhang, Chen's avatar Zhang, Chen Committed by GitHub
Browse files

Numpy 2.x compatible and switch to Pixi (#326) 



* update to np 2.x and switch to pixi

* add pixi lock file

* update pixi for Github actions

* remove outdated action branch

* Update tests/unit/backend/dataio/test_data.py

Co-authored-by: default avatarCopilot <175728472+Copilot@users.noreply.github.com>

* Update tests/unit/backend/dataio/test_data.py

Co-authored-by: default avatarCopilot <175728472+Copilot@users.noreply.github.com>

* Update GitHub Actions workflow to run tests with xvfb and change rotation angle dtype to float64

* fix tomopy upstream issue via duck typing

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci



* disable lint check to allow duck type patching

---------

Co-authored-by: default avatarCopilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: default avatarpre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
parent f0329db4

.github/workflows/actions.yml

+9 −27
Original line number Diff line number Diff line
@@ -15,36 +15,18 @@ jobs: 
        shell: bash -l {0}

    steps:

      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3

      - uses: prefix-dev/setup-pixi@v0.8.2

        with:

          auto-update-conda: true

          mamba-version: "*"

          environment-file: environment.yml

          pixi-version: v0.50.2

          manifest: pyproject.toml

      - name: Verify docstrings

        run: pydocstyle --convention=numpy src/

        run: pixi run pydocstyle --convention=numpy src/

      - name: Install ui test requirements

        run: playwright install

      - name: Install iMars3d in editable mode

        run: pip install -e .

        run: pixi run playwright install

      - name: Tests without data repository

        uses: coactions/setup-xvfb@v1

        with:

          run: |

          python -m pytest --cov --cov-report=xml --cov-report=term -m "not datarepo"

            pixi run pytest -m 'not datarepo' --tb=short -v

      - name: Upload coverage to Codecov

        uses: codecov/codecov-action@v5
 


  build-wheel:

    runs-on: ubuntu-latest

    defaults:

      run:

        shell: bash -l {0}

    steps:

      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3

        with:

          auto-update-conda: true

          mamba-version: "*"

          environment-file: environment.yml

      - name: Build Wheel

        run: python -m build --no-isolation --wheel

      - name: Check Wheel Contents

        run: check-wheel-contents .

.github/workflows/protected_branches.yml

+10 −45
Original line number Diff line number Diff line
@@ -27,13 +27,12 @@ jobs: 
        with:

          submodules: true

          lfs: true

      - uses: conda-incubator/setup-miniconda@v3

      - uses: prefix-dev/setup-pixi@v0.8.2

        with:

          auto-update-conda: true

          miniforge-version: latest

          environment-file: environment.yml

          pixi-version: v0.50.2

          manifest: pyproject.toml

      - name: Tests with data repository

        run: python -m pytest -m datarepo

        run: pixi run pytest -m datarepo

      - name: Update job status

        uses: Sibz/github-status-action@v1

        if: ${{ always() && github.event_name == 'workflow_dispatch' }}
@@ -53,17 +52,14 @@ jobs: 
        shell: bash -l {0}

    steps:

      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3

      - uses: prefix-dev/setup-pixi@v0.8.2

        with:

          auto-update-conda: true

          mamba-version: "*"

          environment-file: environment.yml

          pixi-version: v0.50.2

          manifest: pyproject.toml

      - name: Build Conda Package

        run: |

          # boa uses mamba to resolve dependencies

          cd conda.recipe

          VERSION=$(versioningit ../) conda mambabuild --output-folder . -c conda-forge . || exit 1

          conda verify noarch/imars3d*.tar.bz2 || exit 1

          # Build conda package using pixi

          pixi run conda-build

      - name: Deploy to Anaconda

        shell: bash -l {0}

        if: startsWith(github.ref, 'refs/tags/v')
@@ -75,35 +71,4 @@ jobs: 
          CONDA_LABEL="main"

          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi

          echo pushing ${{ github.ref }} with label $CONDA_LABEL

          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/imars3d*.tar.bz2





  trigger-deploy:

    runs-on: ubuntu-22.04

    needs: [build-conda]

    # only trigger deploys from protected branches

    if: ${{ github.ref_protected || github.ref_type == 'tag' }}

    steps:

      - name: Determine Environment

        uses: neutrons/branch-mapper@v2

        id: conda_env_name

        with:

          prefix: imars3d



      - name: Trigger deploy

        id: trigger

        uses: eic/trigger-gitlab-ci@v3

        with:

          url: https://code.ornl.gov

          token: ${{ secrets.GITLAB_TRIGGER_TOKEN }}

          project_id: 11848

          ref_name: main

          variables: |

            PLAY="update"

            CONDA_ENV="${{ steps.conda_env_name.outputs.name }}"



      - name: Annotate commit

        uses: peter-evans/commit-comment@v3

        with:

          body: |

            GitLab pipeline for ${{ steps.conda_env_name.outputs.name }} has been submitted for this commit: ${{ steps.trigger.outputs.web_url }}
 
          pixi run anaconda upload --label $CONDA_LABEL *.conda

.gitignore

+12 −0
Original line number Diff line number Diff line
@@ -277,3 +277,15 @@ $RECYCLE.BIN/ 
# End of https://www.toptal.com/developers/gitignore/api/python,macos,linux,windows,visualstudiocode

.vscode/settings.json

_version.py



# Pixi

.pixi/

pixi.lock

*.conda

pyproject.toml.bak



# node modules

node_modules/

package-lock.json

package.json

.claude/settings.local.json

.pre-commit-config.yaml

+8 −7
Original line number Diff line number Diff line
@@ -33,12 +33,13 @@ repos: 
    rev: v1.37.1

    hooks:

      - id: yamllint

    name: yamllint

    description: This hook runs yamllint.

    entry: yamllint

    language: python

    types: [file, yaml]

  - repo: https://github.com/kynan/nbstripout

    rev: 0.8.1

    hooks:

      - id: nbstripout

  - repo: https://github.com/astral-sh/ruff-pre-commit

    rev: v0.9.2

    hooks:

      - id: ruff

        args: [--fix]

      - id: ruff-format

docs/conf.py

+2 −1
Original line number Diff line number Diff line
@@ -4,8 +4,9 @@ 
# https://www.sphinx-doc.org/en/master/usage/configuration.html

import os

import sys

import versioningit



import param

import versioningit



param.parameterized.docstring_signature = False

param.parameterized.docstring_describe_params = False