Enable tests for Python 3.10 (#339)

* Enable tests for Python 3.10

* pep 621 pyproject.toml

* Update pyproject.toml

* Exclude pip 22.1

* Update pyproject.toml and  _metadata.py following the lead of anndata

* Fix reference to author in docs

.conda/meta.yaml

@@ -19,6 +19,7 @@ requirements:
   # requires all dependencies to be installed at build time.
   host:
     - python >=3.7
+    - pip!=22.1 # https://github.com/pypa/pip/issues/11110
     - flit
     - setuptools_scm
     - pytoml

.github/workflows/docs.yml

@@ -55,9 +55,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        # TODO this is to workaround an issue with the skbio dependency
-        # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
         run: |
+          # https://github.com/pypa/pip/issues/11110
+          python -m pip install --upgrade "pip!=22.1"
+          # TODO this is to workaround an issue with the skbio dependency
+          # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
           pip install git+https://github.com/grst/scikit-bio.git@a3423e4
           pip install .[doc,test,rpack,dandelion]
       - name: run sphinx

.github/workflows/pythonpublish.yml

@@ -3,7 +3,7 @@ name: Publish on PyPI
 on:
   push:
     tags:
-      - 'v*.*.*'
+      - "v*.*.*"
 
 jobs:
   deploy:
@@ -19,7 +19,8 @@ jobs:
           python-version: "3.8"
       - name: Install dependencies
         run: |
-          python -m pip install flit
+          # https://github.com/pypa/pip/issues/11110
+          python -m pip install flit "pip!=22.1"
           pip install .
       - name: Build and publish
         env:

.github/workflows/test.yml

@@ -17,7 +17,7 @@ jobs:
           - { python-version: 3.7, os: ubuntu-latest }
           - { python-version: 3.8, os: ubuntu-latest }
           - { python-version: 3.9, os: ubuntu-latest }
-          # - { python-version: "3.10", os: ubuntu-latest }
+          - { python-version: "3.10", os: ubuntu-latest }
           - { python-version: 3.9, os: macos-latest }
           - { python-version: 3.9, os: windows-latest }
 
@@ -45,9 +45,11 @@ jobs:
         with:
           python-version: ${{ matrix.config.python-version }}
       - name: Install dependencies
-        # TODO this is to workaround an issue with the skbio dependency
-        # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
         run: |
+          # https://github.com/pypa/pip/issues/11110
+          python -m pip install --upgrade "pip!=22.1"
+          # TODO this is to workaround an issue with the skbio dependency
+          # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
           pip install git+https://github.com/grst/scikit-bio.git@a3423e4
           pip install .[test,rpack,dandelion]
       - name: Check black formatting

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.1.0
+    rev: 22.3.0
     hooks:
       - id: black
         language_version: python3.10

docs/conf.py

@@ -8,16 +8,18 @@
 sys.path.insert(0, str(HERE.parent))
 sys.path.insert(0, str(HERE / "extensions"))
 
-from scirpy import __author__, __version__
+from importlib.metadata import metadata
+
+info = metadata("scirpy")
 
 # ignore Future warnings (which are caused by dependencies)
 warnings.filterwarnings("ignore", category=FutureWarning)
 
 # General information
-project = "scirpy"
-author = __author__
+project = info["Name"]
+author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
-version = __version__
+version = info["Version"]
 
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]

pyproject.toml

@@ -8,12 +8,13 @@ requires = [
 ]
 build-backend = 'flit_core.buildapi'
 
-[tool.flit.metadata]
-module = 'scirpy'
-author = 'Gregor Sturm, Tamas Szabo'
-author-email = 'gregor.sturm@i-med.ac.at'
-home-page = 'https://github.com/grst/scirpy'
-description-file = "README.rst"
+[project]
+name = 'scirpy'
+authors = [
+    {name = "Gregor Sturm", email="gregor.sturm@i-med.ac.at"},
+    {name= "Tamas Szabo"},
+]
+readme = {file = "README.rst", content-type="text/x-rst"}
 classifiers = [
     'License :: OSI Approved :: BSD License',
     'Development Status :: 4 - Beta',
@@ -23,11 +24,11 @@ classifiers = [
     'Programming Language :: R'
 ]
 requires-python = '>= 3.7'
-requires = [
+dependencies = [
     'anndata>=0.7.6',
     'scanpy>=1.6.0',
     'pandas>=1.0',
-    'numpy>=1.17.0', 
+    'numpy>=1.17.0',
     'scipy',
     # parasail 1.2.1 fails to be installd on MacOS
     'parasail != 1.2.1',
@@ -46,8 +47,9 @@ requires = [
     'importlib_metadata>=0.7; python_version < "3.8"',
     'pycairo>=1.20; sys_platform == "win32"',
 ]
+dynamic = ["version", "description"]
 
-[tool.flit.metadata.requires-extra]
+[project.optional-dependencies]
 rpack = [
     'rectangle-packer',
 ]
@@ -78,8 +80,11 @@ doc = [
     'sc-dandelion',
 ]
 
-[tool.flit.metadata.urls]
+[project.urls]
 Documentation = 'https://scverse.org/scirpy/'
+Home-page = 'https://scverse.org/scirpy/'
+Source = "https://github.com/scverse/scirpy"
+
 
 [tool.pytest.ini_options]
 markers = [

scirpy/__init__.py

@@ -1,6 +1,6 @@
 """Python library for single-cell adaptive immune receptor repertoire (AIRR) analysis"""
 
-from ._metadata import __version__, __author__, __email__, within_flit
+from ._metadata import __version__, within_flit
 
 if not within_flit():
     from scanpy import AnnData, read_h5ad

scirpy/_metadata.py

@@ -1,44 +1,45 @@
-"""Metadata. Adapted from https://github.com/theislab/scanpy/pull/1374/."""
 import traceback
 from pathlib import Path
 
 here = Path(__file__).parent
 
+
+def refresh_entry_points():
+    """\
+    Under some circumstances, (e.g. when installing a PEP 517 package via pip),
+    pkg_resources.working_set.entries is stale. This tries to fix that.
+    See https://github.com/pypa/setuptools_scm/issues/513
+    """
+    try:
+        import sys
+        import pkg_resources
+
+        ws: pkg_resources.WorkingSet = pkg_resources.working_set
+        for entry in sys.path:
+            ws.add_entry(entry)
+    except Exception:
+        pass
+
+
 try:
     from setuptools_scm import get_version
-    import pytoml
-
-    proj = pytoml.loads((here.parent / "pyproject.toml").read_text())
-    metadata = proj["tool"]["flit"]["metadata"]
-
-    # The `split` removes the "local" version part (PEP440), e.g. from
-    # 0.6.1.dev5+ga652c20.d20210130. Leaving the local part, results in the following
-    # error message:
-    #    WARNING: Built wheel for scirpy is invalid: Wheel has unexpected file name:
-    #    expected '0.6.1.dev5+ga652c20.d20210130', got '0.6.1.dev5-ga652c20.d20210130'
-    #
-    # TODO I expect this to be a temporary issue with either flit or wheel, as
-    # this has worked before.
-    __version__ = get_version(
-        # Allegedly, the parameters from pyproject.toml should be passed automatically.
-        # However, this didn't work, so I pass them explicitly here.
-        root="..",
-        relative_to=__file__,
-        **proj["tool"]["setuptools_scm"],
-    ).split("+")[0]
-    __author__ = metadata["author"]
-    __email__ = metadata["author-email"]
 
+    refresh_entry_points()
+    __version__ = get_version(root="..", relative_to=__file__)
 except (ImportError, LookupError, FileNotFoundError):
     from ._compat import pkg_metadata
 
     metadata = pkg_metadata(here.name)
     __version__ = metadata["Version"]
-    __author__ = metadata["Author"]
-    __email__ = metadata["Author-email"]
 
 
 def within_flit():
+    """\
+    Checks if we are being imported by flit.
+    This is necessary so flit can import __version__ without all depedencies installed.
+    There are a few options to make this hack unnecessary, see:
+    https://github.com/takluyver/flit/issues/253#issuecomment-737870438
+    """
     for frame in traceback.extract_stack():
         if frame.name == "get_docstring_and_version_via_import":
             return True