Require pinned pynwb version again

TESTING.md

@@ -0,0 +1,29 @@
+# Testing
+
+The tests in the `tests` folder use pytest and can be run locally as:
+
+```
+SKIP_LIMS=true TEST_INHOUSE=false pytest
+```
+
+This does not assume that you have access to AllenInstitute internal resources like LIMS or network shares.
+
+## Strategy for adopting newer NWB schema versions
+
+The upstream source of NWB files for ipfx is [MIES](https://github.com/AllenInstitute/MIES) and
+[IPNWB](https://github.com/AllenInstitute/IPNWB). We are at the moment using fixed versions of nwb-schema for
+IPNWB and pynwb for ipfx. This is done in order to reduce maintenance and friction between the two.
+
+Steps for upgrading:
+
+- Choose a pynwb/nwb-schema version you want to adopt
+- Raise pynwb version in `requirements.txt`
+- Check if all tests still pass. In the past this always required patching the latest
+  pynwb version, bringing that patch upstream and waiting for a new release.
+- Fix pynwb deprecations where appropriate
+- Upgrade the nwb-schema version used in IPNWB as documented there
+- Re-export the files `Vip-IRES-Cre;Ai14(IVSCC)-226110.03.01.pxp` and
+  `Vip-IRES-Cre;Ai14(IVSCC)-236654.04.02.pxp` using the IPNWB/MIES version with the new nwb-schema to NWBv2
+- Add the files to `tests/data` and extend `testdata` in `tests/test_run_feature_vector.py` with them
+- Check if the tests still pass
+- Propose a PR

requirements.txt

@@ -9,7 +9,7 @@ pandas
 pg8000
 pillow
 pyabf
-pynwb
+pynwb==3.1.2
 pyYAML
 ruamel.yaml<0.18.0
 scipy

tests/test_run_feature_vector.py

@@ -14,9 +14,17 @@
 
 nwb2_file1 = os.path.join(current_directory, "data", "Vip-IRES-Cre;Ai14(IVSCC)-226110.03.01.nwb")
 nwb2_file2 = os.path.join(current_directory, "data", "Vip-IRES-Cre;Ai14(IVSCC)-236654.04.02.nwb")
-test_nwb2_files = dict({500844783: nwb2_file1, 509604672: nwb2_file2})
+nwb2_nwb_schema_2_9_0_file1 = os.path.join(current_directory, "data", "Vip-IRES-Cre;Ai14(IVSCC)-226110.03.01_ITC18USB_Dev_0-nwb-schema-2.9.0.nwb")
+nwb2_nwb_schema_2_9_0_file2 = os.path.join(current_directory, "data", "Vip-IRES-Cre;Ai14(IVSCC)-236654.04.02_ITC18USB_Dev_0-nwb-schema-2.9.0.nwb")
 
-def test_feature_vector_extraction(tmpdir_factory):
+testdata = [dict({500844783: nwb2_file1,
+                  509604672: nwb2_file2}),
+            dict({500844783: nwb2_nwb_schema_2_9_0_file1,
+                  509604672: nwb2_nwb_schema_2_9_0_file2})
+           ]
+
+@pytest.mark.parametrize("ids_and_files", testdata, ids = ["default", "schema-2.9.0"])
+def test_feature_vector_extraction(ids_and_files, tmpdir_factory):
 
     temp_output_dir = str(tmpdir_factory.mktemp("feature_vector"))
     test_output_dir = TEST_OUTPUT_DIR
@@ -37,7 +45,7 @@ def test_feature_vector_extraction(tmpdir_factory):
         "subthresh_depol_norm",
         ]
 
-    run_feature_vector_extraction(ids=[500844783, 509604672],
+    run_feature_vector_extraction(ids=ids_and_files.keys(),
                                   output_dir=temp_output_dir,
                                   data_source="filesystem",
                                   output_code="TEMP",
@@ -47,7 +55,7 @@ def test_feature_vector_extraction(tmpdir_factory):
                                   include_failed_cells=True,
                                   run_parallel=False,
                                   ap_window_length=0.003,
-                                  file_list=test_nwb2_files
+                                  file_list=ids_and_files
                                   )
 
     for feature in features:
@@ -57,19 +65,20 @@ def test_feature_vector_extraction(tmpdir_factory):
         assert np.allclose(test_data, temp_data)
 
 
-def test_feature_collection(tmpdir_factory):
+@pytest.mark.parametrize("ids_and_files", testdata, ids = ["default", "schema-2.9.0"])
+def test_feature_collection(ids_and_files, tmpdir_factory):
 
     temp_output_dir = str(tmpdir_factory.mktemp("feature_vector"))
     test_output_dir = TEST_OUTPUT_DIR
 
     temp_output_file = os.path.join(temp_output_dir, "features_T301.csv")
     test_output_file = os.path.join(test_output_dir, "features_T301.csv")
 
-    run_feature_collection(ids=[500844783, 509604672],
+    run_feature_collection(ids=ids_and_files.keys(),
                            output_file=temp_output_file,
                            data_source="filesystem",
                            run_parallel=False,
-                           file_list=test_nwb2_files)
+                           file_list=ids_and_files)
 
     test_table = pd.read_csv(test_output_file, sep=",").to_dict()
     temp_table = pd.read_csv(temp_output_file, sep=",").to_dict()