From 5c12e8d32e9ccc2689eaf49e4e91b337ba273be2 Mon Sep 17 00:00:00 2001 From: Ryan Abernathey Date: Tue, 6 Feb 2024 18:01:20 -0500 Subject: [PATCH 1/3] removed unused environments and workflows --- .github/workflows/minimal.yml | 41 ------------- .github/workflows/python-package.yml | 88 ---------------------------- environment.yml | 14 ----- requirements_dev_minimal.txt | 8 --- requirements_dev_numpy.txt | 4 -- requirements_dev_optional.txt | 23 -------- 6 files changed, 178 deletions(-) delete mode 100644 .github/workflows/minimal.yml delete mode 100644 .github/workflows/python-package.yml delete mode 100644 environment.yml delete mode 100644 requirements_dev_minimal.txt delete mode 100644 requirements_dev_numpy.txt delete mode 100644 requirements_dev_optional.txt diff --git a/.github/workflows/minimal.yml b/.github/workflows/minimal.yml deleted file mode 100644 index 2c0cd45ca9..0000000000 --- a/.github/workflows/minimal.yml +++ /dev/null @@ -1,41 +0,0 @@ -# This workflow simulates the environment found during a conda-forge build -# and makes sure that Zarr can run without fsspec and other additional libraries. -name: Minimal installation - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - minimum_build: - - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2.3.0 - with: - channels: conda-forge - environment-file: environment.yml - activate-environment: minimal - - name: Tests - shell: "bash -l {0}" - env: - ZARR_V3_EXPERIMENTAL_API: 1 - ZARR_V3_SHARDING: 1 - run: | - conda activate minimal - python -m pip install . - pytest -svx --timeout=300 - - name: Fixture generation - shell: "bash -l {0}" - env: - ZARR_V3_EXPERIMENTAL_API: 1 - ZARR_V3_SHARDING: 1 - run: | - conda activate minimal - rm -rf fixture/ - pytest -svx --timeout=300 zarr/tests/test_dim_separator.py zarr/tests/test_storage.py - # This simulates fixture-less tests in conda and debian packaging diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml deleted file mode 100644 index 5775d85c24..0000000000 --- a/.github/workflows/python-package.yml +++ /dev/null @@ -1,88 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Linux Testing - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ['3.10', '3.11'] - numpy_version: ['>=1.22.0', '==1.20.*'] - exclude: - - python-version: '3.10' - numpy_version: '==1.20.*' - - python-version: '3.11' - numpy_version: '==1.20.*' - services: - redis: - image: redis - # Set health checks to wait until redis has started - options: >- - --health-cmd "redis-cli ping" - --health-interval 10s - --health-timeout 5s - --health-retries 5 - ports: - - 6379:6379 - mongodb: - image: mongo:4.4.11 - ports: - - 27017:27017 - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2.3.0 - with: - channels: conda-forge - python-version: ${{ matrix.python-version }} - env: - ACTIONS_ALLOW_UNSECURE_COMMANDS: true - # Runs a set of commands using the runners shell - - name: Create Conda environment with the rights deps - shell: "bash -l {0}" - run: | - conda create -n zarr-env python==${{matrix.python-version}} bsddb3 numcodecs lmdb pip nodejs flake8 mypy - conda activate zarr-env - npm install -g azurite - - name: Install dependencies - shell: "bash -l {0}" - run: | - conda activate zarr-env - python -m pip install --upgrade pip - python -m pip install -U pip setuptools wheel line_profiler - python -m pip install -rrequirements_dev_minimal.txt numpy${{matrix.numpy_version}} -rrequirements_dev_optional.txt pymongo redis - python -m pip install . - python -m pip freeze - - name: Tests - shell: "bash -l {0}" - env: - COVERAGE_FILE: .coverage.${{matrix.python-version}}.${{matrix.numpy_version}} - ZARR_TEST_ABS: 1 - ZARR_TEST_MONGO: 1 - ZARR_TEST_REDIS: 1 - ZARR_V3_EXPERIMENTAL_API: 1 - ZARR_V3_SHARDING: 1 - run: | - conda activate zarr-env - mkdir ~/blob_emulator - azurite -l ~/blob_emulator --debug debug.log 2>&1 > stdouterr.log & - pytest --cov=zarr --cov-config=pyproject.toml --doctest-plus --cov-report xml --cov=./ --timeout=300 - - uses: codecov/codecov-action@v3 - with: - token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos - #files: ./coverage1.xml,./coverage2.xml # optional - #flags: unittests # optional - #name: codecov-umbrella # optional - #fail_ci_if_error: true # optional (default = false) - verbose: true # optional (default = false) diff --git a/environment.yml b/environment.yml deleted file mode 100644 index dc99507427..0000000000 --- a/environment.yml +++ /dev/null @@ -1,14 +0,0 @@ -channels: - - conda-forge - - defaults -dependencies: - - wheel - - numcodecs >= 0.6.4 - - numpy >= 1.20 - - pip - - pip: - - asciitree - - fasteners - - pytest - - pytest-timeout - - setuptools_scm diff --git a/requirements_dev_minimal.txt b/requirements_dev_minimal.txt deleted file mode 100644 index e2be6eb825..0000000000 --- a/requirements_dev_minimal.txt +++ /dev/null @@ -1,8 +0,0 @@ -# library requirements -asciitree==0.3.3 -fasteners==0.19 -numcodecs==0.11.0 -msgpack-python==0.5.6 -setuptools-scm==8.0.4 -# test requirements -pytest==7.4.3 diff --git a/requirements_dev_numpy.txt b/requirements_dev_numpy.txt deleted file mode 100644 index ee8970780a..0000000000 --- a/requirements_dev_numpy.txt +++ /dev/null @@ -1,4 +0,0 @@ -# Break this out into a separate file to allow testing against -# different versions of numpy. This file should pin to the latest -# numpy version. -numpy==1.26.3 diff --git a/requirements_dev_optional.txt b/requirements_dev_optional.txt deleted file mode 100644 index f3ea80a546..0000000000 --- a/requirements_dev_optional.txt +++ /dev/null @@ -1,23 +0,0 @@ -# optional library requirements -# bsddb3==6.2.6; sys_platform != 'win32' -lmdb==1.4.1; sys_platform != 'win32' -# optional library requirements for Jupyter -ipytree==0.2.2 -ipywidgets==8.1.0 -# optional library requirements for services -# don't let pyup change pinning for azure-storage-blob, need to pin to older -# version to get compatibility with azure storage emulator on appveyor (FIXME) -azure-storage-blob==12.16.0 # pyup: ignore -redis==5.0.1 -types-redis -types-setuptools -pymongo==4.5.0 -# optional test requirements -coverage -pytest-cov==4.1.0 -pytest-doctestplus==1.0.0 -pytest-timeout==2.2.0 -h5py==3.10.0 -fsspec==2023.10.0 -s3fs==2023.10.0 -moto[server]>=4.0.8 From 46fc908ff486906d4238cf423624747e8ba7de21 Mon Sep 17 00:00:00 2001 From: Ryan Abernathey Date: Tue, 6 Feb 2024 22:31:31 -0500 Subject: [PATCH 2/3] added v3 contributor guide --- README-v3.md | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 README-v3.md diff --git a/README-v3.md b/README-v3.md new file mode 100644 index 0000000000..3c4226dcb0 --- /dev/null +++ b/README-v3.md @@ -0,0 +1,49 @@ +# V3 Contributor Guide + +A bare-bones guide to contributing to V3. + +Developed for the Feb. 2024 Zarr Sprint. + +## Clone V3 branch + +[Fork](https://github.com/zarr-developers/zarr-python/fork) zarr-python and clone it locally. + +``` +git clone {your remote} +git remote add upstream https://github.com/zarr-developers/zarr-python +git fetch upstream +git checkout --track upstream/v3 +``` + +## Set up your environment + +Zarr uses [hatch](https://hatch.pypa.io/) for its build system. + +``` +mamba install hatch +``` + +or + +``` +pip install hatch +``` + +Then + +``` +hatch env create test +``` + +## Run the Tests + +``` +hatch run test:run +``` + +or + +``` +hatch -e test +pytest -v +``` \ No newline at end of file From ab462f7ce7056e56a22d0e3e297f63f4bfc78634 Mon Sep 17 00:00:00 2001 From: Ryan Abernathey Date: Tue, 6 Feb 2024 22:33:52 -0500 Subject: [PATCH 3/3] add shell --- README-v3.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README-v3.md b/README-v3.md index 3c4226dcb0..8348038e5a 100644 --- a/README-v3.md +++ b/README-v3.md @@ -44,6 +44,6 @@ hatch run test:run or ``` -hatch -e test +hatch -e test shell pytest -v ``` \ No newline at end of file