Fix testing of min and optional requirements (#99)

* Fix testing of min and optional requirements * Update CHANGELOG.md * Update tox.ini * Ignore pkg_resources deprecation warning in test_gallery (#100) * Update test_gallery.py * Update requirements-min.txt * Update setup.py * Update requirements.txt * Use hdmf 3.5.4 only * Update tox.ini * Discard changes to .github/workflows/run_all_tests.yml --------- Co-authored-by: Matthew Avaylon <[email protected]>
hdmf-dev · Jul 12, 2023 · 30219ba · 30219ba
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Showing 6 changed files with 39 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,7 +15,11 @@
 ### Test suite enhancements
 * Modularized unit tests to simplify running tests for multiple Zarr storage backends.
   @oruebel [#62](https://github.com/hdmf-dev/hdmf-zarr/pull/62)
-* Updated tests to handle upcoming changes to ``HDMFIO``. @rly [#102](https://github.com/hdmf-dev/hdmf-zarr/pull/102)
+* Fixed CI testing of minimum and optional installation requirement. @rly
+  [#99](https://github.com/hdmf-dev/hdmf-zarr/pull/99)
+* Updated tests to handle upcoming changes to ``HDMFIO``. @rly 
+  [#102](https://github.com/hdmf-dev/hdmf-zarr/pull/102)
+
 
 ### Docs
 * Added developer documentation on how to integrate new storage backends with ZarrIO. @oruebel

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,6 +1,6 @@
-hdmf==3.5.2
+hdmf==3.5.4
 zarr==2.11.0
 numcodecs==0.9.1
-pynwb==2.0.0
+pynwb==2.3.2
 setuptools
 importlib_resources;python_version<'3.9' # Remove when python 3.9 becomes the new minimum
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
-hdmf==3.5.2
+hdmf==3.5.4
 zarr==2.11.0
-pynwb==2.3.0
+pynwb==2.3.2
 numpy==1.23.5
 numcodecs==0.11.0
diff --git a/setup.py b/setup.py
@@ -17,11 +17,11 @@
 
 
 reqs = [
-    'hdmf<=3.5.4, >=3.5.2',
+    'hdmf==3.5.4',  # temporary
     'zarr>=2.11.0',
     'numpy>=1.22, <1.24; python_version>"3.7"',
     'numcodecs>=0.9.1',
-    'pynwb>=2.0.0',
+    'pynwb>=2.3.2',
     'setuptools',
 ]
 

diff --git a/test_gallery.py b/test_gallery.py
@@ -23,6 +23,14 @@ def _import_from_file(script):
     spec.loader.exec_module(module)
 
 
+_pkg_resources_warning_re = (
+    "pkg_resources is deprecated as an API"
+)
+
+_pkg_resources_declare_warning_re = (
+    r"Deprecated call to `pkg_resources\.declare_namespace.*"
+)
+
 _numpy_warning_re = (
     "numpy.ufunc size changed, may indicate binary incompatibility. Expected 216, got 192"
 )
@@ -111,6 +119,14 @@ def run_gallery_tests():
                     # against a different version of numpy than the one installed
                     "ignore", message=_numpy_warning_re, category=RuntimeWarning
                 )
+                warnings.filterwarnings(
+                    # this warning is triggered when downstream code such as pynwb uses pkg_resources>=5.13
+                    "ignore", message=_pkg_resources_warning_re, category=DeprecationWarning
+                )
+                warnings.filterwarnings(
+                    # this warning is triggered when downstream code such as pynwb uses pkg_resources>=5.13
+                    "ignore", message=_pkg_resources_declare_warning_re, category=DeprecationWarning
+                )
                 _import_from_file(script_abs)
         except Exception:
             print(traceback.format_exc())

diff --git a/tox.ini b/tox.ini
@@ -14,7 +14,7 @@ setenv =
   PYTHONDONTWRITEBYTECODE = 1
   VIRTUALENV_python -m pip = 22.3.1
 install_command =
-    python -m pip install -U {opts} {packages}
+    python -m pip install {opts} {packages}
 
 deps =
     -rrequirements-dev.txt
@@ -37,7 +37,8 @@ basepython = python3.11
 install_command =
     python -m pip install {opts} {packages}
 deps =
-    -rrequirements-dev.txt
+    {[testenv]deps}
+    # -rrequirements-opt.txt
 commands = {[testenv]commands}
 
 # Test with python 3.11; pinned dev and optional reqs; upgraded run reqs
@@ -47,6 +48,7 @@ install_command =
     python -m pip install -U {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    # -rrequirements-opt.txt
 commands = {[testenv]commands}
 
 # Test with python 3.11; pinned dev and optional reqs; upgraded, pre-release run reqs
@@ -56,6 +58,7 @@ install_command =
     python -m pip install -U --pre {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    # -rrequirements-opt.txt
 commands = {[testenv]commands}
 
 # Test with python 3.7; pinned dev reqs; minimum run reqs
@@ -95,7 +98,8 @@ commands = {[testenv:build]commands}
 [testenv:build-py311-optional]
 basepython = python3.11
 deps =
-    -rrequirements-dev.txt
+    {[testenv]deps}
+    # -rrequirements-opt.txt
 commands = {[testenv:build]commands}
 
 [testenv:build-py311-upgraded]
@@ -104,6 +108,7 @@ install_command =
     python -m pip install -U {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    # -rrequirements-opt.txt
 commands = {[testenv:build]commands}
 
 [testenv:build-py311-prerelease]
@@ -112,6 +117,7 @@ install_command =
     python -m pip install -U --pre {opts} {packages}
 deps =
     -rrequirements-dev.txt
+    # -rrequirements-opt.txt
 commands = {[testenv:build]commands}
 
 [testenv:build-py37-minimum]
@@ -129,7 +135,7 @@ commands = python -c "import hdmf_zarr"
 # Envs that will execute gallery tests
 [testenv:gallery]
 install_command =
-    python -m pip install -U {opts} {packages}
+    python -m pip install {opts} {packages}
 
 deps =
     -rrequirements-dev.txt
@@ -167,6 +173,7 @@ install_command =
 deps =
     -rrequirements-dev.txt
     -rrequirements-doc.txt
+    # -rrequirements-opt.txt
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.11; pinned dev, doc, and optional reqs; pre-release run reqs
@@ -177,6 +184,7 @@ install_command =
 deps =
     -rrequirements-dev.txt
     -rrequirements-doc.txt
+    # -rrequirements-opt.txt
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.7; pinned dev and doc reqs; minimum run reqs