updates envs

NeurodataWithoutBorders · Dec 9, 2024 · 8e901d0 · 8e901d0
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commit 8e901d0
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Showing 4 changed files with 30 additions and 23 deletions.
diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml
@@ -7,19 +7,21 @@ dependencies:
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
-  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - jsonschema = 4.18.0 # installs jsonschema-specifications
   - pip
   - pip:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - tables
diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml
@@ -7,11 +7,11 @@ dependencies:
   - nodejs = 18.16.1
   # Install these from conda-forge so that dependent packages get included in the distributable
   - numcodecs = 0.11.0
-  - lxml = 4.9.3  # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
-  - pyedflib = 0.1.32  # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
-  - numpy  # May have x64/arm64 mismatch issues so install from conda-forge
+  - lxml = 4.9.3 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
+  - pyedflib = 0.1.32 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
+  - numpy # May have x64/arm64 mismatch issues so install from conda-forge
   - pytables = 3.8 # PyPI build fails on arm64 so install from conda-forge (used by neuroconv deps)
-  - jsonschema = 4.18.0  # Also installs jsonschema-specifications
+  - jsonschema = 4.18.0 # Also installs jsonschema-specifications
   - pip
   - pip:
       - setuptools==70.0.0
@@ -21,13 +21,14 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install
       # NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml
@@ -7,7 +7,7 @@ dependencies:
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
-  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - jsonschema = 4.18.0 # installs jsonschema-specifications
   - pip
   - pip:
       - setuptools==70.0.0
@@ -18,11 +18,13 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - tables
diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
@@ -12,17 +12,19 @@ dependencies:
   - pip:
       - setuptools==70.0.0
       - PyInstaller==6.7.0
-      - pyinstaller-hooks-contrib == 2024.6  # Fix needed for pydantic v2; otherwise imports pydantic.compiled
+      - pyinstaller-hooks-contrib == 2024.6 # Fix needed for pydantic v2; otherwise imports pydantic.compiled
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - tables