Merge pull request #53 from ISA-tools/test_upgrade

Test upgrade

Author: proccaserra

.github/workflows/package.yml

@@ -6,49 +6,54 @@ on:
       - v*.*.*
 
 jobs:
-
   wheel:
     runs-on: ubuntu-latest
-    name: Build universal wheel
+    name: Build wheel
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         submodules: true
-    - name: Setup Python 3.9
-      uses: actions/setup-python@v2
+    - name: Setup Python 3.14
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.14'
+        cache: pip
     - name: Install build requirements
-      run: python -m pip install -r ci/requirements.txt
+      run: |
+        python -m pip install -U pip wheel setuptools
+        python -m pip install -r ci/requirements.txt
     - name: Build wheel
-      run: python setup.py bdist_wheel
+      run: python -m build --wheel
     - name: Store built wheels
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: dist
+        name: dist-wheel
         path: dist/*
 
   sdist:
     runs-on: ubuntu-latest
     name: Build source distribution
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         submodules: true
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.14
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.14'
+        cache: pip
     - name: Install build requirements
-      run: python -m pip install -r ci/requirements.txt
-    - name: Build wheel distribution
-      run: python setup.py sdist
+      run: |
+        python -m pip install -U pip wheel setuptools
+        python -m pip install -r ci/requirements.txt
+    - name: Build source distribution
+      run: python -m build --sdist
     - name: Store built wheels
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
-        name: dist
+        name: dist-sdist
         path: dist/*
 
   upload:
@@ -60,13 +65,14 @@ jobs:
     - wheel
     steps:
     - name: Download built distributions
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
-          name: dist
+          pattern: dist-*
           path: dist
+          merge-multiple: true
     - name: Publish distributions to PyPI
       if: startsWith(github.ref, 'refs/tags/v')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
@@ -80,7 +86,7 @@ jobs:
     needs: upload
     steps:
     - name: Checkout code
-      uses: actions/checkout@v1
+      uses: actions/checkout@v4
       with:
         submodules: true
     - name: Release a Changelog

.github/workflows/test.yml

@@ -5,43 +5,45 @@ on:
   - pull_request
 
 jobs:
-
   test-linux:
     name: Test (Linux)
     runs-on: ubuntu-latest
     env:
-      OS: Linux
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     strategy:
       matrix:
         python-version:
-          - '3.6'
-          - '3.7'
-          - '3.8'
           - '3.9'
           - '3.10'
+          - '3.11'
+          - '3.12'
+          - '3.13'
+          - '3.14'
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         submodules: true
     - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Update pip
-      run: python -m pip install -U pip wheel setuptools
-    - name: Install Python requirements
-      run: python -m pip install -r ci/requirements.txt
-    - name: Install library
-      run: python -m pip install .
-    - name: Install test requirements
-      run: python -m pip install -U -r tests/requirements.txt
+        cache: pip
+    - name: Install dependencies
+      run: |
+        python -m pip install -U pip wheel setuptools
+        python -m pip install -r ci/requirements.txt
+        python -m pip install -e .[test]
     - name: Test with coverage
       run: python -m coverage run -m unittest discover -vv
     - name: Upload to Codecov
-      uses: codecov/codecov-action@v1
+      if: ${{ env.CODECOV_TOKEN != '' }}
+      uses: codecov/codecov-action@v4
       with:
         flags: ${{ matrix.python-version }}
         name: test-python-${{ matrix.python-version }}
         fail_ci_if_error: true
-        token: ${{ secrets.CODECOV_TOKEN }}
+        token: ${{ env.CODECOV_TOKEN }}
+    - name: Skip Codecov upload
+      if: ${{ env.CODECOV_TOKEN == '' }}
+      run: echo "CODECOV_TOKEN is not set; skipping Codecov upload."

.gitignore

@@ -86,6 +86,8 @@ celerybeat-schedule
 # virtualenv
 venv/
 ENV/
+.venv/
+.venv310/
 
 # Spyder project settings
 .spyderproject

ci/requirements.txt

@@ -1,8 +1,7 @@
-coverage
-codecov
-green
-pip
-setuptools
-wheel
-twine
+build >=1.2,<2
+coverage >=7.6,<8
+pip >=25,<26
+setuptools >=69
+twine >=6,<7
+wheel >=0.45,<1
 pyinstaller>=3.6 ; sys_platform == 'win32'

mzml2isa/_fs.py

@@ -0,0 +1,14 @@
+"""Helpers for importing PyFilesystem without noisy deprecation warnings."""
+
+import warnings
+
+
+with warnings.catch_warnings():
+    warnings.filterwarnings(
+        "ignore",
+        message=r"pkg_resources is deprecated as an API\.",
+        category=UserWarning,
+    )
+    import fs
+    import fs.errors
+    import fs.path

mzml2isa/_impl.py

@@ -1,18 +1,8 @@
-"""Conditional imports of optional dependencies.
-"""
+"""Compatibility helpers for supported Python versions."""
 
-# --- Available Cache --------------------------------------------------------
-
-try:
-    from functools import cache
-except ImportError:
-    from functools import lru_cache
-    cache = lru_cache(maxsize=None)
-
-try:
-    from functools import cached_property
-except ImportError:
-    from cached_property import cached_property
+from contextlib import contextmanager
+from functools import cache
+from functools import cached_property
 
 
 # --- Available XML parser ---------------------------------------------------
@@ -47,15 +37,8 @@ def get_parent(element, tree):
 
 # --- Available package resources --------------------------------------------
 
-try:
-    import importlib.resources as importlib_resources
-except ImportError:
-    import importlib_resources
-
-try:
-    from importlib.resources import files as resource_files
-except ImportError:
-    from importlib_resources import files as resource_files
+import importlib.resources as importlib_resources
+from importlib.resources import files as resource_files
 
 
 # --- Optional progress bar --------------------------------------------------
@@ -64,3 +47,25 @@ def get_parent(element, tree):
     import tqdm
 except ImportError:
     tqdm = None
+
+
+@contextmanager
+def pronto_no_multiprocessing():
+    """Force pronto to parse ontologies without creating multiprocessing pools."""
+    import pronto.utils.pool as pronto_pool
+
+    thread_pool = pronto_pool._ThreadPool
+    pronto_pool._ThreadPool = None
+    try:
+        yield
+    finally:
+        pronto_pool._ThreadPool = thread_pool
+
+
+def load_pronto_ontology(pronto_module, filename):
+    """Load a pronto ontology, falling back to sequential parsing if needed."""
+    try:
+        return pronto_module.Ontology(filename)
+    except PermissionError:
+        with pronto_no_multiprocessing():
+            return pronto_module.Ontology(filename)

mzml2isa/imzml.py

@@ -16,7 +16,7 @@
 import pronto
 
 from . import ontologies
-from ._impl import importlib_resources
+from ._impl import cache, importlib_resources, load_pronto_ontology
 from .mzml import _CVParameter, MzMLFile
 
 
@@ -33,10 +33,13 @@ class ImzMLFile(MzMLFile):
         }
     )
 
-    with warnings.catch_warnings(record=True): 
-        warnings.simplefilter('ignore', pronto.warnings.SyntaxWarning)
-        with importlib_resources.path(ontologies.__name__, "imagingMS.obo") as filename:
-            _VOCABULARY = pronto.Ontology(filename)
+    @classmethod
+    @cache
+    def _default_vocabulary(cls):
+        with warnings.catch_warnings(record=True):
+            warnings.simplefilter("ignore", pronto.warnings.SyntaxWarning)
+            with importlib_resources.path(ontologies.__name__, "imagingMS.obo") as filename:
+                return load_pronto_ontology(pronto, filename)
 
     @classmethod
     def _assay_parameters(cls):

mzml2isa/isa.py

@@ -15,10 +15,10 @@
 """
 import os
 import csv
-import pkg_resources
 import re
 import sys
 import functools
+import copy
 from collections import ChainMap
 
 from . import (
@@ -61,12 +61,13 @@ def __init__(self, out_dir, name, usermeta=None, **kwargs):
                 "a_imzML.txt" in your custom template directory. If None, the uses the
                 ones shipping with mzml2isa, compatible with MetaboLights [default: None]
         """
-        usermeta = kwargs.get('usermeta', None)
+        usermeta = kwargs.get('usermeta', usermeta)
         template_default = resource_files(templates.__name__)
         template_directory = kwargs.get('template_directory') or template_default
 
         # Create one or several study files / one or several study section in investigation
-        self.usermeta = usermeta or {}
+        self.usermeta = copy.deepcopy(usermeta) if usermeta is not None else {}
+        self._set_default_usermeta(name)
         self.isa_env = {
             'out_dir': out_dir,
             'Study Identifier':  name,
@@ -86,6 +87,23 @@ def __init__(self, out_dir, name, usermeta=None, **kwargs):
         self.isa_env['Converter'] = __name__
         self.isa_env['Converter version'] = __version__
 
+    def _set_default_usermeta(self, name):
+        """Populate minimal study metadata required by ISA validators."""
+        defaults = {
+            'investigation': {
+                'title': name,
+                'description': "Generated from mzML metadata by mzml2isa.",
+            },
+            'study': {
+                'title': name,
+                'description': "Generated from mzML metadata by mzml2isa.",
+            },
+        }
+        for section, values in defaults.items():
+            target = self.usermeta.setdefault(section, {})
+            for key, value in values.items():
+                target.setdefault(key, value)
+
     def write(self, metalist, datatype, **kwargs):
         """Generate and write the ISA files