Migrate to the new takane specification (#1)

* Save and Load Summarized and RangedSummarized Experiments
* Export common utils for reuse in SE derivatives
* Update tests, documentation and github actions

.github/workflows/pypi-publish.yml

@@ -1,3 +1,6 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
 name: Publish to PyPI
 
 on:
@@ -6,32 +9,43 @@ on:
 
 jobs:
   build:
+
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-
+    - uses: actions/checkout@v2
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-        cache: 'pip'
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest tox
-
+        pip install flake8 pytest tox
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with tox
       run: |
         tox
-
-    - name: Build package
+    - name: Build docs
+      run: |
+        tox -e docs
+    - run: touch ./docs/_build/html/.nojekyll
+    - name: GH Pages Deployment
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages # The branch the action should deploy to.
+        folder: ./docs/_build/html
+        clean: true # Automatically remove deleted files from the deploy branch
+    - name: Build Project and Publish
       run: |
         python -m tox -e clean,build
-
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -2,29 +2,36 @@ name: Test the library
 
 on:
   push:
-    branches:
-      - master
+    branches: [ master ]
   pull_request:
+    branches: [ master ]
 
 jobs:
   build:
+
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
 
+    name: Python ${{ matrix.python-version }}
     steps:
-      - name: Check out repo
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-          cache: 'pip'
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox
-  
-      - name: Test with tox
-        run: |
-          tox
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest tox
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with tox
+      run: |
+        tox

setup.cfg

@@ -5,17 +5,17 @@
 
 [metadata]
 name = dolomite-se
-description = Add a short description here!
+description = Save and load summarized experiments in the dolomite framework!
 author = LTLA
 author_email = [email protected]
 license = MIT
 license_files = LICENSE.txt
 long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
-url = https://github.com/pyscaffold/pyscaffold/
+url = https://github.com/ArtifactDB/dolomite-se
 # Add here related links, for example:
 project_urls =
-    Documentation = https://pyscaffold.org/
+    Documentation = https://github.com/ArtifactDB/dolomite-se
 #    Source = https://github.com/pyscaffold/pyscaffold/
 #    Changelog = https://pyscaffold.org/en/latest/changelog.html
 #    Tracker = https://github.com/pyscaffold/pyscaffold/issues
@@ -41,17 +41,18 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-# python_requires = >=3.8
+python_requires = >=3.8
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite_base
-    dolomite_matrix
-    summarizedexperiment>=0.3.7
+    dolomite_base==0.2.0-alpha6
+    dolomite_matrix==0.1.0-alpha3
+    dolomite_ranges==0.0.1-alpha2
+    summarizedexperiment>=0.4.2,<0.5.0
 
 
 [options.packages.find]
@@ -70,7 +71,6 @@ testing =
     pytest
     pytest-cov
     numpy
-    filebackedarray
 
 [options.entry_points]
 # Add here console scripts like:

src/dolomite_se/__init__.py

@@ -15,5 +15,8 @@
 finally:
     del version, PackageNotFoundError
 
-from .stage_summarized_experiment import stage_summarized_experiment
-from .load_summarized_experiment import load_summarized_experiment
+from .read_summarized_experiment import read_summarized_experiment
+from .save_summarized_experiment import save_summarized_experiment
+from .save_ranged_summarized_experiment import save_ranged_summarized_experiment
+from .read_ranged_summarized_experiment import read_ranged_summarized_experiment
+from .utils import save_common_se_props, read_common_se_props

src/dolomite_se/read_ranged_summarized_experiment.py

@@ -0,0 +1,58 @@
+import os
+
+import dolomite_base as dl
+from dolomite_base.read_object import read_object_registry
+from summarizedexperiment import RangedSummarizedExperiment
+
+from .utils import read_common_se_props
+
+read_object_registry[
+    "ranged_summarized_experiment"
+] = "dolomite_se.read_ranged_summarized_experiment"
+
+
+def read_ranged_summarized_experiment(
+    path: str, metadata: dict, **kwargs
+) -> RangedSummarizedExperiment:
+    """Load a
+    :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`
+    from its on-disk representation.
+
+    This method should generally not be called directly but instead be invoked by
+    :py:meth:`~dolomite_base.read_object.read_object`.
+
+    Args:
+        path:
+            Path to the directory containing the object.
+
+        metadata:
+            Metadata for the object.
+
+        kwargs:
+            Further arguments, ignored.
+
+    Returns:
+        A
+        :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`
+        with file-backed arrays in the assays.
+    """
+
+    _row_data, _column_data, _assays = read_common_se_props(path)
+
+    rse = RangedSummarizedExperiment(
+        assays=_assays,
+        row_data=_row_data,
+        column_data=_column_data,
+    )
+
+    _meta_path = os.path.join(path, "other_data")
+    if os.path.exists(_meta_path):
+        _meta = dl.read_object(_meta_path)
+        rse = rse.set_metadata(_meta.as_dict())
+
+    _ranges_path = os.path.join(path, "row_ranges")
+    if os.path.exists(_ranges_path):
+        _ranges = dl.read_object(_ranges_path)
+        rse = rse.set_row_ranges(_ranges)
+
+    return rse