Add icephys meta (#1349)

Declare SweepTable as deprecated on init Add TimeSeriesReferenceVectorData Container class Add simple test for TimeSeriesReferenceVectorData Update nwb-schema branch Add icephys metadata container classes Update NWBFile to support icephys metadata tables Add unit tests for icephys metadata tables Update imports and fix SweepTable integration tests Fix test available namespaces testcase Update SweepTable tutorial and declare as deprecated Add new icephys tutorial using the new hierarchical metadata tables Add IntracellularRecordingsTable illustration Fix flake8 issues Remove use of HierarchiclaDynamicTableMixin use for now Add source PowerPoint file for icephys docs add doc for TimeIntervals (#1352) * add doc for TimeIntervals * add allensdk back Fix make clean command for docs to also clean sphinx-gallery files Updated CHANGELOG to describe changes from this PR Add thumbnails for domain-specfic tutorials Add thumbnaisl for general tutorials Update changelog Remove ic_filtering/icephys_filtering duplicate and fix test Fix description of ExperimentalConditionsTable Use HDMF 2.5.0 (#1354) DOC: make template less puzzling in how to fill out ;-) (#1336) Co-authored-by: Ryan Ly <[email protected]> Add ReadTheDocs badge to README (#1311) Co-authored-by: Ryan Ly <[email protected]> Update to use upcoming HDMF 2.5.1 (#1355) Revert breaking changes to scratch API (#1356) Use HDMF 2.5.2 (#1360) Add `DfOverF` to docs (#1351) Co-authored-by: Ryan Ly <[email protected]> docs/gallery/general/file.py: Fix argument count in documentation add strain optional arg to Subject (#1241) * remove validate_core_schema. You can check the core schema with e.g. * Update Subject unit test * Fix Subject unit test, add check for date_of_birth Co-authored-by: Ryan Ly <[email protected]> add source channels to DecompSeries add option to include source_channels for DecompositionSeries (#1258) * add option to include source_channels for DecompositionSeries and include round trip test * Use latest schema * Add unit test Add optional link to Device in ImageSeries (#1265) * Add optional link to Device in ImageSeries * Add support for device in ImageSeries subclasses * Update ImageMaskSeries docstring * Update schema add continuity optional arg to TimeSeries.__init__ (#1226) * add continuity optional arg to TimeSeries.__init__ * use new enum feature of hdmf to check against controlled vocabulary * Fix flake8 * Add integration test * Fix flake8 * Add correct mapping for data.continuity Co-authored-by: Ryan Ly <[email protected]> Add support for ElectricalSeries.filtering dataset (#1270) Set fixed value for IZeroClampSeries stimulus description Fix test Update changelog Add note about allensdk py3.8 incompatibility Add workaround for validation against cached hdmf-experimental Update CI to avoid click8 incompatibility Use HDMF 2.5.5 Address comments, improve doc Fix docs, add citation info, update repo infra (#1362) Use latest HDMF, raise min pandas, dissociate req-min and setup reqs (#1363) Use nwb schema branch for icephys meta Ensure start_index and count are set to -1 if TimeSeries is None Add test for conversion of start_index and index_count vals Fix flake8 in __compute_index docstring Fix icephys metadata roundtrip NWBFile test base on update DynamicTableRegion behavior Update schema (updated version to 1.4.0-alpha) improve extensions documentation (#1350) * improve extensions documentation * adjustments to extensions.rst * add tips to extension docs * create multi-part extensions tutorial * move API building docs to chapter 5 of extensions guide * restructure and fix up some spots * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/6_documenting_extension.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <[email protected]> * remove detailed GroupSpec API instructions from tutorial * remove instructions for generated the directory structure, and instead focus on generating the HTML and filling in the missing pieces. * add link to ndx catalog * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/4_auto_api.rst * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <[email protected]> * Update extensions_tutorial_home.rst * Minor text fixes * Minor text fixes * Minor text fixes Co-authored-by: Oliver Ruebel <[email protected]> Co-authored-by: Ryan Ly <[email protected]> Set language for code block to fix readthedocs Add RRID for PyNWB Add RRID to README Update changelog make MotionCorrection test (#1374) * attempt to make MotionCorrection test. I don't understand why it's failing * Fix CorrectedImageStack nwbfields * Fix tests * Fix test * Fix flake8 * Fix test Co-authored-by: Ryan Ly <[email protected]> Add unique electrode id check (#1344) Co-authored-by: Ryan Ly <[email protected]> Fix integration tests with invalid test data that will be caught by future hdmf validator version (#1366) Co-authored-by: Ryan Ly <[email protected]> Improve documentation and test for CorrectedImageStack (#1306) Fix test for validator update (#1376) Update changelog Allow h5py 3 so that this can work with hdmf rc/3.0.0 Move SweepTable DeprectationWarning to the constructor of SweepTable to clean up code Suppress SweepTable Deprecation warning in icephys integration test Ignore and assert deprecation warning for SweepTable during SweepTable roundtrip tests Merge branch 'rc/2.0.0' into add/icephys_meta Fix falke8 on icephys tutorial galleries
NeurodataWithoutBorders · Aug 10, 2021 · e905aa2 · e905aa2
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -38,13 +38,6 @@ references:
         username: hdmf
         password: $DOCKERHUB_PASSWORD
 
-  py36: &py36
-    docker:
-    - image: circleci/python:3.6.13-buster
-      auth:
-        username: hdmf
-        password: $DOCKERHUB_PASSWORD
-
   conda-image: &conda-image
     docker:
     - image: continuumio/miniconda3:4.9.2
@@ -161,14 +154,6 @@ jobs:
       - run:
           <<: *run-style-check
 
-  python36:
-    <<: *py36
-    environment:
-      - TEST_TOX_ENV: "py36"
-      - BUILD_TOX_ENV: "build-py36"
-      - TEST_WHEELINSTALL_ENV: "wheelinstall"
-    <<: *ci-steps
-
   python37:
     <<: *py37
     environment:
@@ -183,7 +168,6 @@ jobs:
       - TEST_TOX_ENV: "py38"
       - BUILD_TOX_ENV: "build-py38"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
-      - UPLOAD_WHEELS: "true"
     <<: *ci-steps
 
   python39:
@@ -192,41 +176,33 @@ jobs:
       - TEST_TOX_ENV: "py39"
       - BUILD_TOX_ENV: "build-py39"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
+      - UPLOAD_WHEELS: "true"  # upload distributions from only this job to pypi
     <<: *ci-steps
 
-  python38-upgrade-dev:
-    <<: *py38
+  python39-upgrade-dev:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "py38-upgrade-dev"
-      - BUILD_TOX_ENV: "build-py38-upgrade-dev"
+      - TEST_TOX_ENV: "py39-upgrade-dev"
+      - BUILD_TOX_ENV: "build-py39-upgrade-dev"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  python38-upgrade-dev-pre:
-    <<: *py38
+  python39-upgrade-dev-pre:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "py38-upgrade-dev-pre"
-      - BUILD_TOX_ENV: "build-py38-upgrade-dev-pre"
+      - TEST_TOX_ENV: "py39-upgrade-dev-pre"
+      - BUILD_TOX_ENV: "build-py39-upgrade-dev-pre"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  python36-min-req:
-    <<: *py36
+  python37-min-req:
+    <<: *py37
     environment:
-      - TEST_TOX_ENV: "py36-min-req"
-      - BUILD_TOX_ENV: "build-py36-min-req"
+      - TEST_TOX_ENV: "py37-min-req"
+      - BUILD_TOX_ENV: "build-py37-min-req"
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *ci-steps
 
-  miniconda36:
-    <<: *conda-image
-    environment:
-      - CONDA_PYTHON_VER: "3.6.*=*_cpython"  # avoid using pypy compiler
-      - TEST_TOX_ENV: "py36"
-      - BUILD_TOX_ENV: "build-py36"
-      - TEST_WHEELINSTALL_ENV: "wheelinstall"
-    <<: *conda-steps
-
   miniconda37:
     <<: *conda-image
     environment:
@@ -254,12 +230,6 @@ jobs:
       - TEST_WHEELINSTALL_ENV: "wheelinstall"
     <<: *conda-steps
 
-  gallery36:
-    <<: *py36
-    environment:
-      - TEST_TOX_ENV: "gallery-py36"
-    <<: *gallery-steps
-
   gallery37:
     <<: *py37
     environment:
@@ -278,26 +248,26 @@ jobs:
       - TEST_TOX_ENV: "gallery-py39"
     <<: *gallery-steps
 
-  gallery38-upgrade-dev:
-    <<: *py38
+  gallery39-upgrade-dev:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "gallery-py38-upgrade-dev"
+      - TEST_TOX_ENV: "gallery-py39-upgrade-dev"
     <<: *gallery-steps
 
-  gallery38-upgrade-dev-pre:
-    <<: *py38
+  gallery39-upgrade-dev-pre:
+    <<: *py39
     environment:
-      - TEST_TOX_ENV: "gallery-py38-upgrade-dev-pre"
+      - TEST_TOX_ENV: "gallery-py39-upgrade-dev-pre"
     <<: *gallery-steps
 
-  gallery36-min-req:
-    <<: *py36
+  gallery37-min-req:
+    <<: *py37
     environment:
-      - TEST_TOX_ENV: "gallery-py36-min-req"
+      - TEST_TOX_ENV: "gallery-py37-min-req"
     <<: *gallery-steps
 
   test-validation:
-    <<: *py38
+    <<: *py39
     steps:
       - checkout
       - run: git submodule sync
@@ -309,13 +279,13 @@ jobs:
           command: |
             . ../venv/bin/activate
             pip install tox
-            tox -e validation-py38
+            tox -e validation-py39
           # Install is expected to be quick. Increase timeout in case there are some network issues.
           # While pip installing tox does not output by default. Circle thinks task is dead after 10 min.
           no_output_timeout: 30m
 
   deploy-dev:
-    <<: *py38
+    <<: *py39
     steps:
       - checkout
       - attach_workspace:
@@ -336,7 +306,7 @@ jobs:
                 --exit-success-if-missing-token
 
   deploy-release:
-    <<: *py38
+    <<: *py39
     steps:
       - attach_workspace:
           at: ./
@@ -354,7 +324,8 @@ jobs:
           command: |
             python -m venv ../venv
             . ../venv/bin/activate
-            pip install githubrelease
+            # use click<8 until https://github.com/j0057/github-release/issues/62 is resolved
+            pip install "click<8" githubrelease
             githubrelease release $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME \
               create $CIRCLE_TAG --name $CIRCLE_TAG \
               --publish ./dist/*
@@ -365,27 +336,27 @@ workflows:
     jobs:
       - flake8:
           <<: *no_filters
-      - python38:
+      - python37-min-req:
           <<: *no_filters
-      - python36-min-req:
+      - python39:
           <<: *no_filters
-      - miniconda36:
+      - miniconda37:
           <<: *no_filters
-      - miniconda38:
+      - miniconda39:
           <<: *no_filters
-      - gallery38:
+      - gallery37-min-req:
           <<: *no_filters
-      - gallery36-min-req:
+      - gallery38:  # TODO replace with gallery39 after allensdk support py39
           <<: *no_filters
       - deploy-dev:
           requires:
             - flake8
-            - python38
-            - python36-min-req
-            - miniconda36
-            - miniconda38
-            - gallery38
-            - gallery36-min-req
+            - python37-min-req
+            - python39
+            - miniconda37
+            - miniconda39
+            - gallery37-min-req
+            - gallery38  # gallery39
           filters:
             tags:
               ignore:
@@ -399,12 +370,12 @@ workflows:
       - deploy-release:
           requires:
             - flake8
-            - python38
-            - python36-min-req
-            - miniconda36
-            - miniconda38
-            - gallery38
-            - gallery36-min-req
+            - python37-min-req
+            - python39
+            - miniconda37
+            - miniconda39
+            - gallery37-min-req
+            - gallery38  # gallery39
           filters:
             tags:
               only: /^[0-9]+(\.[0-9]+)*(\.post[0-9]+)?$/
@@ -423,41 +394,33 @@ workflows:
     jobs:
       - flake8:
           <<: *no_filters
-      - python36:
-          <<: *no_filters
       - python37:
           <<: *no_filters
+      - python37-min-req:
+          <<: *no_filters
       - python38:
           <<: *no_filters
       - python39:
           <<: *no_filters
-      - python38-upgrade-dev:
-          <<: *no_filters
-      - python36-min-req:
+      - python39-upgrade-dev:
           <<: *no_filters
-      - miniconda36:
+      - python39-upgrade-dev-pre:
           <<: *no_filters
       - miniconda37:
           <<: *no_filters
       - miniconda38:
           <<: *no_filters
       - miniconda39:
           <<: *no_filters
-      - gallery36:
-          <<: *no_filters
       - gallery37:
           <<: *no_filters
+      - gallery37-min-req:
+          <<: *no_filters
       - gallery38:
           <<: *no_filters
       - gallery39:
           <<: *no_filters
-      - gallery38-upgrade-dev:
-          <<: *no_filters
-      - gallery36-min-req:
-          <<: *no_filters
-      - python38-upgrade-dev-pre:
-          <<: *no_filters
-      - gallery38-upgrade-dev-pre:
+      - gallery39-upgrade-dev:
           <<: *no_filters
-      - test-validation:
+      - gallery39-upgrade-dev-pre:
           <<: *no_filters
diff --git a/.coveragerc b/.coveragerc
@@ -3,4 +3,10 @@ branch = True
 source = src/
 omit =
     src/pynwb/_version.py
+    src/pynwb/_due.py
     src/pynwb/testing/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    @abstract
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -20,13 +20,14 @@ assignees: ''
 <!--Please describe your environment according to the following bullet points.-->
 
     Python Executable: Conda or Python
-    Python Version: Python 3.5, 3.6, or 3.7
+    Python Version: Python 3.7, 3.8, or 3.9
     Operating System: Windows, macOS or Linux
-    HDMF Version: Version of PyNWB used
+    HDMF Version:
+    PyNWB Version:
 
 ## Checklist
 
-- [ ] Have you ensured the feature or change was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?
+- [ ] Have you ensured the bug was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?
 - [ ] Have you included a brief and descriptive title?
 - [ ] Have you included a clear description of the problem you are trying to solve?
 - [ ] Have you included a minimal code snippet that reproduces the issue you are encountering?

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -4,13 +4,14 @@ What was the reasoning behind this change? Please explain the changes briefly.
 
 ## How to test the behavior?
 ```
-Show here how to reproduce the new behavior (can be a bug fix or a new feature)
+Show how to reproduce the new behavior (can be a bug fix or a new feature)
 ```
 
 ## Checklist
 
+- [ ] Did you update CHANGELOG.md with your changes?
 - [ ] Have you checked our [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?
-- [ ] Have you ensured the PR description clearly describes problem and the solution?
+- [ ] Have you ensured the PR clearly describes the problem and the solution?
 - [ ] Is your contribution compliant with our coding style? This can be checked running `flake8` from the source directory.
 - [ ] Have you checked to ensure that there aren't other open [Pull Requests](https://github.com/NeurodataWithoutBorders/pynwb/pulls) for the same change?
-- [ ] Have you included the relevant issue number using `#XXX` notation where `XXX` is the issue number?
+- [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.
diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md
@@ -0,0 +1,26 @@
+Prepare for release of PyNWB [version]
+
+### Before merging:
+- [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
+  `requirements-doc.txt`, `requirements-min.txt`, `setup.py` as needed
+  See https://requires.io/github/NeurodataWithoutBorders/pynwb/requirements/?branch=dev
+- [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
+  and any other locations as needed
+- [ ] Update `setup.py` as needed
+- [ ] Update `README.rst` as needed
+- [ ] Update `src/pynwb/nwb-schema` submodule as needed. Check the version number and commit SHA manually
+- [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed
+- [ ] Run tests locally including gallery tests and validation tests, and inspect all warnings and outputs
+  (`python test.py -v > out.txt`)
+- [ ] Test docs locally (`make apidoc`, `make html`)
+- [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged
+- [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and
+  build docs for new branch): https://readthedocs.org/projects/pynwb/builds/
+
+### After merging:
+1. Create release by following steps in `docs/source/make_a_release.rst` or use alias `git pypi-release [tag]` if set up
+2. After the CI bot creates the new release (wait ~10 min), update the release notes on the
+   [GitHub releases page](https://github.com/NeurodataWithoutBorders/pynwb/releases) with the changelog
+3. Check that the readthedocs "latest" and "stable" builds run and succeed
+4. Update [conda-forge/pynwb-feedstock](https://github.com/conda-forge/pynwb-feedstock) with the latest version number
+   and SHA256 retrieved from PyPI > PyNWB > Download Files > View hashes for the `.tar.gz` file. Re-render as needed
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -15,7 +15,7 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     env:
       OS: ${{ matrix.os }}
-      PYTHON: '3.8'
+      PYTHON: '3.9'
     steps:
     - name: Cancel Workflow Action
       uses: styfle/[email protected]
@@ -27,7 +27,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.gitignore b/.gitignore
@@ -59,6 +59,9 @@ docs/tmpl.index.rst
 tests/coverage/htmlcov
 .coverage
 
+# duecredit output
+.duecredit.p
+
 # tox
 .tox