From f9c2fd06b5ac9008cce8e4e5222b91e454fa4597 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:37:42 -0400 Subject: [PATCH 01/14] remove non testing installations --- environments/environment-Windows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml index 1cb6f2e23..237ffb190 100644 --- a/environments/environment-Windows.yml +++ b/environments/environment-Windows.yml @@ -18,7 +18,7 @@ dependencies: - flask == 2.3.2 - flask-cors === 3.0.10 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] - dandi >= 0.60.0 - pytest == 7.2.2 - pytest-cov == 4.1.0 From 603a68d64f0c58ceaa5887ab31f9352a18c01e63 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:40:39 -0400 Subject: [PATCH 02/14] add notes to various manual dependencies --- environments/environment-Windows.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml index 237ffb190..e26b38e9a 100644 --- a/environments/environment-Windows.yml +++ b/environments/environment-Windows.yml @@ -19,9 +19,6 @@ dependencies: - flask-cors === 3.0.10 - flask_restx == 1.1.0 - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] - - dandi >= 0.60.0 - - pytest == 7.2.2 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling From 290b63ab40074c336adbed408d440f8e7e799caa Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:41:04 -0400 Subject: [PATCH 03/14] copy to other platforms --- environments/environment-MAC-intel.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml index 3cb937767..75d060825 100644 --- a/environments/environment-MAC-intel.yml +++ b/environments/environment-MAC-intel.yml @@ -18,10 +18,7 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling From 4103c591990808c62e6bd156dd5931b933471d7d Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:41:20 -0400 Subject: [PATCH 04/14] copy to other platforms --- environments/environment-Linux.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml index ea486f110..91e201373 100644 --- a/environments/environment-Linux.yml +++ b/environments/environment-Linux.yml @@ -15,10 +15,7 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling From 2f46626d75ddbafbe52b0307b9ce5001ba4128df Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:43:35 -0400 Subject: [PATCH 05/14] copy to other platforms --- .../environment-MAC-apple-silicon.yml | 27 +++++++++---------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml index 39daf9452..99eb52dcd 100644 --- a/environments/environment-MAC-apple-silicon.yml +++ b/environments/environment-MAC-apple-silicon.yml @@ -5,13 +5,13 @@ channels: dependencies: - python = 3.9.18 - 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 - - pytables = 3.8 # pypi build fails on arm64 so install from conda-forge (used by neuroconv deps) - # install these from conda-forge so that dependent packages get included in the distributable - - jsonschema = 4.18.0 # installs jsonschema-specifications + - 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 - pip - pip: - setuptools==70.0.0 @@ -21,12 +21,9 @@ dependencies: - flask == 2.3.2 - flask-cors == 4.0.0 - flask_restx == 1.1.0 - # 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 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - dandi >= 0.60.0 - - pytest == 7.4.0 - - pytest-cov == 4.1.0 - - scikit-learn == 1.4.0 - - tqdm_publisher >= 0.0.1 - - tzlocal >= 5.2 + # 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 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[dandi,compressors,ecephys,ophys,behavior,text] + - scikit-learn == 1.4.0 # Tutorial data generation + - tqdm_publisher >= 0.0.1 # Progress bars + - tzlocal >= 5.2 # Frontend timezone handling From 37f01d854cb9b6ba0bb8d93a736208e6c8e52872 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:44:47 -0400 Subject: [PATCH 06/14] move to CI --- .github/workflows/testing_dev.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml index 731f3968d..5348f3d7b 100644 --- a/.github/workflows/testing_dev.yml +++ b/.github/workflows/testing_dev.yml @@ -74,6 +74,9 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + - if: matrix.os != 'ubuntu-latest' name: Run tests run: npm run test:coverage From f32f9bd2cb7b64e3f20f6c39ec7c22dc006b1b82 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:45:20 -0400 Subject: [PATCH 07/14] move to CI --- .github/workflows/testing_flask_build_and_dist.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml index 83f483cf5..1a07623e9 100644 --- a/.github/workflows/testing_flask_build_and_dist.yml +++ b/.github/workflows/testing_flask_build_and_dist.yml @@ -79,7 +79,11 @@ jobs: with: node-version: "20" - - run: npm ci --verbose + - name: Install GUIDE + run: npm ci --verbose + + - name: Install testing dependencies + run: pip install pytest pytest-cov # Fix for macos build - remove bad sonpy file - if: matrix.os == 'macos-latest' || matrix.os == 'macos-13' From 10d5b11fcec17c88c4688d385cd6b9b039098ae3 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:45:37 -0400 Subject: [PATCH 08/14] move to CI --- .github/workflows/testing_dev_with_live_services.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml index b44c90c8d..3bf53239a 100644 --- a/.github/workflows/testing_dev_with_live_services.yml +++ b/.github/workflows/testing_dev_with_live_services.yml @@ -76,6 +76,9 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + - name: Create env file run: | touch .env From 85ae7b28eaae926538cccf0a212c12e685f08993 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 13:46:03 -0400 Subject: [PATCH 09/14] move to CI --- .github/workflows/testing_pipelines.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml index f8e5022e9..851134adb 100644 --- a/.github/workflows/testing_pipelines.yml +++ b/.github/workflows/testing_pipelines.yml @@ -72,6 +72,9 @@ jobs: - name: Install GUIDE run: npm ci --verbose + - name: Install testing dependencies + run: pip install pytest pytest-cov + # Load example data caches - name: Get ephy_testing_data current head hash id: ephys From 3fb3533249abfe407fe41d02c9b50e2653e6b715 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 17:47:54 -0400 Subject: [PATCH 10/14] Update testing_flask_build_and_dist.yml --- .github/workflows/testing_flask_build_and_dist.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml index 1a07623e9..6c75e116b 100644 --- a/.github/workflows/testing_flask_build_and_dist.yml +++ b/.github/workflows/testing_flask_build_and_dist.yml @@ -85,6 +85,9 @@ jobs: - name: Install testing dependencies run: pip install pytest pytest-cov + - name: Manually remove matplotlib + run: pip uninstall matplotlib + # Fix for macos build - remove bad sonpy file - if: matrix.os == 'macos-latest' || matrix.os == 'macos-13' run: rm -f "$CONDA_PREFIX/lib/python3.9/site-packages/sonpy/linux/sonpy.so" From a47feb28bfae13d9af8a0d13eb79b78705ad0ff6 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 17:48:09 -0400 Subject: [PATCH 11/14] Update testing_dev.yml --- .github/workflows/testing_dev.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml index 5348f3d7b..c532d1cf9 100644 --- a/.github/workflows/testing_dev.yml +++ b/.github/workflows/testing_dev.yml @@ -77,6 +77,9 @@ jobs: - name: Install testing dependencies run: pip install pytest pytest-cov + - name: Manually remove matplotlib + run: pip uninstall matplotlib + - if: matrix.os != 'ubuntu-latest' name: Run tests run: npm run test:coverage From e6867b45dad0e65dd6a65cca025fa23737b882b3 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 17:48:20 -0400 Subject: [PATCH 12/14] Update testing_dev_with_live_services.yml --- .github/workflows/testing_dev_with_live_services.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml index 3bf53239a..c4b76425b 100644 --- a/.github/workflows/testing_dev_with_live_services.yml +++ b/.github/workflows/testing_dev_with_live_services.yml @@ -79,6 +79,9 @@ jobs: - name: Install testing dependencies run: pip install pytest pytest-cov + - name: Manually remove matplotlib + run: pip uninstall matplotlib + - name: Create env file run: | touch .env From 6551ebbb7e39240943b162330ad40806bbae198b Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Sun, 4 Aug 2024 17:48:36 -0400 Subject: [PATCH 13/14] Update testing_pipelines.yml --- .github/workflows/testing_pipelines.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml index 851134adb..268be3551 100644 --- a/.github/workflows/testing_pipelines.yml +++ b/.github/workflows/testing_pipelines.yml @@ -75,6 +75,9 @@ jobs: - name: Install testing dependencies run: pip install pytest pytest-cov + - name: Manually remove matplotlib + run: pip uninstall matplotlib + # Load example data caches - name: Get ephy_testing_data current head hash id: ephys From a6b4c7e56c4a953c3902bd507e7c9a30588fc8d3 Mon Sep 17 00:00:00 2001 From: CodyCBakerPhD Date: Sun, 4 Aug 2024 20:48:04 -0400 Subject: [PATCH 14/14] --yes --- .github/workflows/testing_dev.yml | 2 +- .github/workflows/testing_dev_with_live_services.yml | 2 +- .github/workflows/testing_flask_build_and_dist.yml | 2 +- .github/workflows/testing_pipelines.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml index c532d1cf9..95b32f068 100644 --- a/.github/workflows/testing_dev.yml +++ b/.github/workflows/testing_dev.yml @@ -78,7 +78,7 @@ jobs: run: pip install pytest pytest-cov - name: Manually remove matplotlib - run: pip uninstall matplotlib + run: pip uninstall matplotlib --yes - if: matrix.os != 'ubuntu-latest' name: Run tests diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml index c4b76425b..1e2e90042 100644 --- a/.github/workflows/testing_dev_with_live_services.yml +++ b/.github/workflows/testing_dev_with_live_services.yml @@ -80,7 +80,7 @@ jobs: run: pip install pytest pytest-cov - name: Manually remove matplotlib - run: pip uninstall matplotlib + run: pip uninstall matplotlib --yes - name: Create env file run: | diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml index 6c75e116b..401a7470e 100644 --- a/.github/workflows/testing_flask_build_and_dist.yml +++ b/.github/workflows/testing_flask_build_and_dist.yml @@ -86,7 +86,7 @@ jobs: run: pip install pytest pytest-cov - name: Manually remove matplotlib - run: pip uninstall matplotlib + run: pip uninstall matplotlib --yes # Fix for macos build - remove bad sonpy file - if: matrix.os == 'macos-latest' || matrix.os == 'macos-13' diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml index 268be3551..c39f258d5 100644 --- a/.github/workflows/testing_pipelines.yml +++ b/.github/workflows/testing_pipelines.yml @@ -76,7 +76,7 @@ jobs: run: pip install pytest pytest-cov - name: Manually remove matplotlib - run: pip uninstall matplotlib + run: pip uninstall matplotlib --yes # Load example data caches - name: Get ephy_testing_data current head hash