From 8a0027f5347fd8439daf1d6ea5bdb97fd47d524c Mon Sep 17 00:00:00 2001 From: TomNicholas Date: Sun, 20 Oct 2024 11:32:03 -0400 Subject: [PATCH 01/10] add new CI workflow --- .github/workflows/upstream.yml | 60 ++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 .github/workflows/upstream.yml diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml new file mode 100644 index 00000000..9140896b --- /dev/null +++ b/.github/workflows/upstream.yml @@ -0,0 +1,60 @@ +name: upstream + +on: + push: + branches: [ "main" ] + paths-ignore: + - 'docs/**' + pull_request: + branches: [ "main" ] + paths-ignore: + - 'docs/**' + schedule: + - cron: "0 0 * * *" + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + + test: + name: ${{ matrix.python-version }}-build + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + strategy: + matrix: + python-version: ["3.12"] + steps: + - uses: actions/checkout@v4 + + - name: Setup micromamba + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: ci/upstream.yml + cache-environment: true + create-args: >- + python=${{matrix.python-version}} + + - name: Install virtualizarr + run: | + python -m pip install -e . --no-deps + - name: Conda list information + run: | + conda env list + conda list + + - name: Running Tests + run: | + python -m pytest ./virtualizarr --cov=./ --cov-report=xml --verbose + + - name: Upload code coverage to Codecov + uses: codecov/codecov-action@v3.1.4 + with: + file: ./coverage.xml + flags: unittests + env_vars: OS,PYTHON + name: codecov-umbrella + fail_ci_if_error: false From 18c8e7cef93f8173c5f7df5b5c4106c38b12a530 Mon Sep 17 00:00:00 2001 From: TomNicholas Date: Sun, 20 Oct 2024 11:32:24 -0400 Subject: [PATCH 02/10] add environment with various bleeding edge branches --- ci/upstream.yml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 ci/upstream.yml diff --git a/ci/upstream.yml b/ci/upstream.yml new file mode 100644 index 00000000..18dab2fe --- /dev/null +++ b/ci/upstream.yml @@ -0,0 +1,28 @@ +name: virtualizarr-min-deps +channels: + - conda-forge + - nodefaults +dependencies: + - h5netcdf + - h5py + - hdf5 + - netcdf4 + - numpy>=2.0.0 + - packaging + - ujson + - universal_pathlib + # Testing + - codecov + - pre-commit + - mypy + - ruff + - pandas-stubs + - pytest-mypy + - pytest-cov + - pytest + - pooch + - fsspec +- pip: + - zarr==3.0.0b1 + - git+https://github.com/pydata/xarray@zarr-v3 + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs \ No newline at end of file From c812f1e8909e70057406b7b7b533a874b3912fda Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 20 Oct 2024 15:34:22 +0000 Subject: [PATCH 03/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ci/upstream.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index 18dab2fe..a66b9a28 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -25,4 +25,4 @@ dependencies: - pip: - zarr==3.0.0b1 - git+https://github.com/pydata/xarray@zarr-v3 - - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs \ No newline at end of file + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs From 889da879c6007027caa08fb4413aa4f8dbedd486 Mon Sep 17 00:00:00 2001 From: TomNicholas Date: Sun, 20 Oct 2024 11:35:26 -0400 Subject: [PATCH 04/10] fix bad yaml formatting --- ci/upstream.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index a66b9a28..401844eb 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -22,7 +22,7 @@ dependencies: - pytest - pooch - fsspec -- pip: - - zarr==3.0.0b1 - - git+https://github.com/pydata/xarray@zarr-v3 - - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs +pip: + - zarr==3.0.0b1 + - git+https://github.com/pydata/xarray@zarr-v3 + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs From d4403f3983af552ccf43832d85c6472e92e17505 Mon Sep 17 00:00:00 2001 From: TomNicholas Date: Sun, 20 Oct 2024 12:09:24 -0400 Subject: [PATCH 05/10] install pip via conda and correct indentation again --- ci/upstream.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index 401844eb..a3b49f7c 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -22,7 +22,8 @@ dependencies: - pytest - pooch - fsspec -pip: - - zarr==3.0.0b1 - - git+https://github.com/pydata/xarray@zarr-v3 - - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs + - pip: + pip: + - zarr==3.0.0b1 + - git+https://github.com/pydata/xarray@zarr-v3 + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs From 496796e4341fbfdfee14f7f8af890c94b90dc663 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 20 Oct 2024 16:09:32 +0000 Subject: [PATCH 06/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ci/upstream.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index a3b49f7c..d8a82539 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -23,7 +23,7 @@ dependencies: - pooch - fsspec - pip: - pip: + pip: - zarr==3.0.0b1 - git+https://github.com/pydata/xarray@zarr-v3 - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs From 4778bdada1f706da556af939bb39e21d4012cceb Mon Sep 17 00:00:00 2001 From: TomNicholas Date: Sun, 20 Oct 2024 12:11:42 -0400 Subject: [PATCH 07/10] formatting again --- ci/upstream.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index a3b49f7c..a55307b8 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -22,8 +22,8 @@ dependencies: - pytest - pooch - fsspec - - pip: - pip: + - pip + - pip: - zarr==3.0.0b1 - git+https://github.com/pydata/xarray@zarr-v3 - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs From 7dfbe100cb18cd5a288ba0a3175cc56fa659487e Mon Sep 17 00:00:00 2001 From: Tom Nicholas Date: Sun, 20 Oct 2024 14:20:13 -0600 Subject: [PATCH 08/10] Note about kerchunk --- ci/upstream.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/ci/upstream.yml b/ci/upstream.yml index 388d4017..702ac093 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -27,3 +27,4 @@ dependencies: - zarr==3.0.0b1 - git+https://github.com/pydata/xarray@zarr-v3 - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs + # - git+https://github.com/fsspec/kerchunk@main # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516) From cbee10354142c6fd1ec909e475026f624d420451 Mon Sep 17 00:00:00 2001 From: Tom Nicholas Date: Sun, 20 Oct 2024 14:21:40 -0600 Subject: [PATCH 09/10] Add comments about zarr-python v3 compatibility branches --- ci/upstream.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index 702ac093..cac1100c 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -24,7 +24,7 @@ dependencies: - fsspec - pip - pip: - - zarr==3.0.0b1 - - git+https://github.com/pydata/xarray@zarr-v3 - - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs + - zarr==3.0.0b1 # beta release of zarr-python v3 + - git+https://github.com/pydata/xarray@zarr-v3 # zarr-v3 compatibility branch + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs # zarr-v3 compatibility branch # - git+https://github.com/fsspec/kerchunk@main # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516) From 61b463ebb948443ecaa46d6fb8a587f5e4faae72 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 20 Oct 2024 20:21:45 +0000 Subject: [PATCH 10/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ci/upstream.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/upstream.yml b/ci/upstream.yml index cac1100c..184c6710 100644 --- a/ci/upstream.yml +++ b/ci/upstream.yml @@ -25,6 +25,6 @@ dependencies: - pip - pip: - zarr==3.0.0b1 # beta release of zarr-python v3 - - git+https://github.com/pydata/xarray@zarr-v3 # zarr-v3 compatibility branch - - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs # zarr-v3 compatibility branch + - git+https://github.com/pydata/xarray@zarr-v3 # zarr-v3 compatibility branch + - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs # zarr-v3 compatibility branch # - git+https://github.com/fsspec/kerchunk@main # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516)