Merge pull request #54 from Becksteinlab/doc-updates

Updating documentation and cleaning up unused files
Becksteinlab · Jul 20, 2024 · 4366f59 · 4366f59
2 parents 9318ecd + c99c2fd
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diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -0,0 +1,126 @@
+name: Build and upload to PyPI
+
+on:
+    pull_request:
+      branches:
+        - "package-*"
+    push:
+      branches:
+        - "package-*"
+      tags:
+        - "package-*"
+    release:
+        types:
+            - published
+
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
+  cancel-in-progress: true
+
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+
+jobs:
+  build_wheels:
+    if: github.repository == 'Becksteinlab/zarrtraj'
+    name: Build wheels
+    runs-on: ${{ matrix.buildplat[0] }}
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        buildplat:
+          - [ubuntu-22.04, manylinux_x86_64, x86_64]
+          - [macos-11, macosx_*, x86_64]
+          - [windows-2019, win_amd64, AMD64]
+          - [macos-14, macosx_*, arm64]
+        python: ["cp310", "cp311", "cp312"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.19.2
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_BUILD_VERBOSITY: 1
+
+      - name: upload artifacts
+        if: |
+            (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
+            (github.event_name == 'release' && github.event.action == 'published')
+        uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    if: github.repository == 'Becksteinlab/zarrtraj'
+    name: build package source distribution
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: upload artifacts
+        if: |
+            (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
+            (github.event_name == 'release' && github.event.action == 'published')
+        uses: actions/upload-artifact@v4
+        with:
+          path: ./dist/*.tar.gz
+          retention-days: 7
+
+  upload_testpypi_zarrtraj:
+    if: github.repository == 'Becksteinlab/zarrtraj' &&
+        (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
+    name: testpypi_upload_zarrtraj
+    environment:
+      name: publisher
+      url: https://test.pypi.org/p/zarrtraj
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      - name: upload_source_and_wheels
+        uses: pypa/[email protected]
+        with:
+          skip-existing: true
+          repository-url: https://test.pypi.org/legacy/
+
+  upload_pypi_zarrtraj:
+    if: | 
+      github.repository == 'Becksteinlab/zarrtraj' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    name: pypi_upload_zarrtraj
+    environment:
+      name: publisher
+      url: https://pypi.org/p/zarrtraj
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      - name: upload_source_and_wheels
+        uses: pypa/[email protected]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,23 @@ The rules for this file:
     * YYYY-MM-DD date format (following ISO 8601)
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
+## [0.2.0]
+
+
+### Authors
+- ljwoods2
+
+### Added
+- Rewrite of repository, zarrtraj supports reading H5MD-formatted files
+
+### Fixed
+
+
+### Changed
+
+
+### Deprecated
+- Proprietary zarrtraj format no longer supported
 
 ## [0.1.0]
 

diff --git a/README.md b/README.md
@@ -21,70 +21,14 @@ zarrtraj
 [url_license]: https://www.gnu.org/licenses/gpl-2.0
 [url_mda]: https://www.mdanalysis.org
 
-This is a kit that provides the ability to read and write trajectory data in the Zarr file format. For more information on the format and usage,
-see the [zarrtraj documentation](https://zarrtraj.readthedocs.io/en/latest/index.html)
+This is an MDAKit that provides the ability to read and write H5MD-formatted trajectory data into MDAnalysis using Zarr. 
+Zarrtraj can read local H5MD files, H5MD files in S3 buckets, and files served via http or https.
+It can read both [H5MD-formatted files stored in hdf5](https://www.nongnu.org/h5md/h5md.html) and [H5MD-formatted files stored 
+in Zarr](https://zarrtraj.readthedocs.io/en/latest/zarrmd-file-spec/v0.1.0.html) (.zarrmd files).
 
-zarrtraj is bound by a [Code of Conduct](https://github.com/Becksteinlab/zarrtraj/blob/main/CODE_OF_CONDUCT.md).
-
-### Installation
-
-To build zarrtraj from source,
-we highly recommend using virtual environments.
-If possible, we strongly recommend that you use
-[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
-Below we provide instructions both for `conda` and
-for `pip`.
-
-#### With conda
-
-Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
-
-Create a virtual environment and activate it:
-
-```
-conda create --name zarrtraj
-conda activate zarrtraj
-```
-
-Install the development and documentation dependencies:
-
-```
-conda env update --name zarrtraj --file devtools/conda-envs/test_env.yaml
-conda env update --name zarrtraj --file docs/requirements.yaml
-```
-
-Build this package from source:
+For more information on installation and usage, see the [zarrtraj documentation](https://zarrtraj.readthedocs.io/en/latest/index.html)
 
-```
-pip install -e .
-```
-
-If you want to update your dependencies (which can be risky!), run:
-
-```
-conda update --all
-```
-
-And when you are finished, you can exit the virtual environment with:
-
-```
-conda deactivate
-```
-
-#### With pip
-
-To build the package from source, run:
-
-```
-pip install .
-```
-
-If you want to create a development environment, install
-the dependencies required for tests and docs with:
-
-```
-pip install ".[test,doc]"
-```
+zarrtraj is bound by a [Code of Conduct](https://github.com/Becksteinlab/zarrtraj/blob/main/CODE_OF_CONDUCT.md).
 
 ### Copyright
 

diff --git a/benchmarks/reader_bms.py b/benchmarks/reader_bms.py
@@ -22,11 +22,11 @@
 
 Development:
 
-    asv run -q -v -e <commit> > bm.log &
+    asv run -q -v -e <branch>^! > bm.log &
 
 Full run:
 
-    asv run -v -e <commit> > bm.log &
+    asv run -v -e <branch>^! > bm.log &
 
 4. To publish, use
 

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -12,16 +12,15 @@ dependencies:
   - zarr>=2.11.0
   - kerchunk>=0.2.6
   - h5py>=3.11.0
-  - dask
 
   ### AWS dependencies ###
   # AWS reading/writing
-  - s3fs=2024.3.0 
+  - s3fs>=2024.3.0 
   - aiobotocore=2.12.1
   - botocore>=1.34.41,<1.34.52
   - boto3>=1.9.201
   # AWS testing
-  - moto=5.0.3
+  - moto>=5.0.3
 
   ### General testing ###
   - MDAnalysisTests>=2.7.0
@@ -30,9 +29,6 @@ dependencies:
   - pytest-cov>=4.1.0
   - codecov
 
-  ### Notebooks ###
-  - jupyter
-
 
   # Pip-only installs
   # - pip: