Relax networkx pin requirement

.github/workflows/test.yaml

@@ -0,0 +1,31 @@
+name: Tests
+on:
+  push:
+  pull_request:
+concurrency:
+  group: test-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.9', '3.13']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache tox env
+        uses: actions/cache@v4
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ hashFiles('requirements-tests.txt') }}-test
+      - name: Install tox
+        run: pip install tox
+      - name: Install test data
+        run: git clone -b tests --single-branch https://github.com/ISA-tools/ISAdatasets tests/data
+      - name: Run tox
+        run: tox

.gitignore

@@ -9,6 +9,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 env/
+.venv/
 build/
 develop-eggs/
 dist/
@@ -120,4 +121,4 @@ features/test_outputs
 .java-version
 
 # never commit test data directory, as it comes from ISA-tools/ISAdatasets!
-tests/data
+tests/data

isatools/isatab_meta.py

@@ -309,13 +309,13 @@ def _get_value(self, base_column, object_column_group, row):
            offset_2r_col.startswith('Term Accession Number'):
             value = OntologyAnnotation(term=str(cell_value))
             term_source_value = row[offset_1r_col]
-            if term_source_value is not '':
+            if term_source_value != '':
                 try:
                     value.term_source = self.ontology_sources[term_source_value]
                 except KeyError:
                     log.debug('term source: %s not found', term_source_value)
             term_accession_value = row[offset_2r_col]
-            if term_accession_value is not '':
+            if term_accession_value != '':
                 value.term_accession = str(term_accession_value)
             return value, None
         try:
@@ -332,14 +332,14 @@ def _get_value(self, base_column, object_column_group, row):
                 unit_term_value = OntologyAnnotation(term=category_key)
                 self.unit_categories[category_key] = unit_term_value
                 unit_term_source_value = row[offset_2r_col]
-                if unit_term_source_value is not '':
+                if unit_term_source_value != '':
                     try:
                         unit_term_value.term_source = self.ontology_sources[
                             unit_term_source_value]
                     except KeyError:
                         log.debug('term source: %s not found', unit_term_source_value)
                 term_accession_value = row[offset_3r_col]
-                if term_accession_value is not '':
+                if term_accession_value != '':
                     unit_term_value.term_accession = term_accession_value
             return cell_value, unit_term_value
         else:

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools>=77.0.1"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "isa-rwval"
+version = "0.10.11"
+authors = [
+    {name = "ISA Infrastructure Team", email = "isatools@googlegroups.com"},
+]
+description = """Metadata tracking tools help to manage an increasingly diverse \
+    set of life science, environmental and biomedical experiments"""
+readme = "README.md"
+license = "CPAL-1.0"
+license-files = ["LICENSE.txt"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: System Administrators",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+requires-python = ">= 3.9"
+dependencies = [
+    "networkx>=2.5",
+]
+
+[project.optional-dependencies]
+viz = ["matplotlib"]
+tables = [
+  "numpy",
+  "pandas",
+]
+
+[project.urls]
+Homepage = "https://isa-tools.org/"
+Documentation = "https://isa-tools.org/isa-api/"
+Repository = "https://github.com/ISA-tools/isa-rwval"
+
+[tool.setuptools]
+packages = [
+    "isatools",
+    "isatools.errors",
+]
+
+[tool.setuptools.package-data]
+isatools = []

tox.ini

@@ -1,15 +1,6 @@
 [tox]
-envlist = py36
+envlist = py
 
 [testenv]
 deps = -rrequirements-tests.txt
-commands=py.test --basetemp=tests
-
-[travis]
-python =
-  3.6: py36
-
-[pytest]
-addopts = --ignore=setup.py
-python_files = *.py
-python_functions = test_
+commands=pytest {posargs}