Update ci workflow #1371
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Update ci workflow #1371
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@@ Coverage Diff @@
## liezl/update_environment_creation #1371 +/- ##
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Coverage ? 72.69%
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talmo
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Jun 28, 2023
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| - test_args: --durations=-1 tests/ | ||
| # Mac specific values | ||
| - os: macos-latest | ||
| env_file: environment_mac.yml | ||
| # Ubuntu specific values | ||
| - os: ubuntu-22.04 | ||
| test_args: --cov=sleap --cov-report=xml --durations=-1 tests/ |
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great idea to handle os-specific flags!
roomrys
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Jun 30, 2023
* First 'working' env for 1.3.1, no GPU... * First working 1.3.1 w/gpu * Sorry, this is the first gpu working env * Fix `imgstore` version-dependent bug * Build and entry points work, but pip packages not installed * Add default channels in condarc.yaml * Rename environment.yaml to .yml * Working build no gpu (documented) * Env working w/gpu using tensorflow from pypi * Working build with GPU! And pip dep * Attempt to fix cannot find wheel ~= 0.35 issue * Run constrain everything * Use minimal conda req for install_requires, inc build number to get it working * Ubuntu build and environments working * Env creation working on M2 * Build and env working on windows (again) * Apple silicon (M2) build working * Pip package working (M2) * Exclude tests and docs from pypi wheel * Add comments to requirements * Get ready for manual build * Update os images, trigger dev build * Retry manual build win and mac * Retry mac manual build (to upload) * Require latest pynwb, remove setuptools * Remove old mac environment * Add twine as a build dependency * Add comments to manual build * Update build.yml * Rename "apple_silicon" to "mac" * Update installation docs (#1365) * Update installation docs * Trigger website build * Update quick install and build docs * Add Mambaforge links * Remove comment about experimental apple silicon support Co-authored-by: Talmo Pereira <[email protected]> * Fix minor typo * Change installation docs to reference universal mac env --------- Co-authored-by: Talmo Pereira <[email protected]> * More flexible with python version ~=3.7 * Pin py3.7.12 for host and run (good on win) * Add comments for why python ~=3.7 * Update ci workflow (#1371) * Update CI workflow to include mac * Trigger CI workflow * Remove verbose? python version * Migrate to micromamba * Explicitly state environment name * Remove environment chaching (for now) * Use different environment file for mac * Use correct syntax * Add `env_hash` and `bash -l {0}` * Remove env_file * Try different nested variable call via format * Use correct syntax * Update env file reference AS -> mac * Different path to environment file * Checkout repo * Use default shells * Remove unused comments * Fix caching attempt by changing caching key * Remove environment caching * Increase python in no_cuda to 3.7.17 * Less restrictive with python ~3.7 version * More direct installation docs 🤞 * Increase build numbers for develop branch build --------- Co-authored-by: Talmo Pereira <[email protected]>
roomrys
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Jun 30, 2023
* Disable data caching by default for SingleImageVideos (#1243) * Disable data caching by default for SingleImageVideos * Remove a couple things that shouldn't be in this PR :) * Centralize video extensions (#1244) * Add video extension support lists to io.video module * Use centralized extension definitions * Remove some unused code * Add some coverage for indirect coverage reduction * Fix single frame GUI increment (#1254) * Fix frame increment for single frame videos * Add test and lint * Add video search to "robustify" (excessively) fragile test (#1262) Add video search to fix fragile test * Organize docks (#1265) * Add `DockWidget` class and subclasses * Create docks in `MainWindow` using `DockWidget` classes * Remove unused imports * Fix references in existing tests * Fix intermittent bug (file-corruption) that has snuck into the tests (#1267) * Remove corrupted test file * Add non-corrupted copy of test file * Rename the file so tests run * Layout docks in a tab configuration (instead of stacked) (#1289) * Add tab with to docks (and use `self.model` in table) * Use `self.model_type` in `create_models` * Increase GUI crop size range from 512 to 832 (#1295) * Fix conversion to numpy array when last frame(s) do not have labels (#1307) * Ensure frames to predict list is unique (#1293) * Ensure frames to predict list is unique * Ensure frames to predict on are ordered correctly * Better frame sorting * Fix GUI resume training (#1314) * Do not choose `top_k` instances if `max_instances` < num centroids (#1313) * Use max_instances as a max without any minimum requirement * Create test (that fails) * Fix test by re-init inference model each call * Do not compute top k if max is greater * Add `--max_instances` to `sleap-track` and GUI (#1305) * Expose --max_instances to sleap-track and in GUI * Lint * Change shorthand to `-n` for both `sleap-export` and `sleap-track` * Add test for creating predictor from cli * Add max instances support to bottom up model (#1306) * Add max instances support to bottom up model * Remove unnecessary attribute setter in CLI parser * Edge case * Expose max_instances for BU to train/infer GUI --------- Co-authored-by: roomrys <[email protected]> * Update docs for `--max_instances` command * Add test for BU `--max_instances` --------- Co-authored-by: Talmo Pereira <[email protected]> * Remove `--labels` and redundant `data_path` (#1326) * Create copy of config info to modify (gui) (#1325) * Fixes GPU memory polling using environment variable filtering (#1272) * add cuda visible gpus to nvidia smi CLI * tests masked none, single and multiple GPUs * deal with comma separated lists and test 2 gpus * clean up system script and better test that actually works * add a case for cuda_visible_devices = [] * add test for gpu order and length in nvidia and tf * test nvidia smi indices and checking gpu memory * fix spaces * fix linting with Black * put skips in tests for git not having nvidia-smi * add doc strings to get_gpu_memory * set CUDA device order to PCI BUS ID * test with no nvidia smi + invalid visible devices * fixed linting again * remove pci env variable, move to other issue --------- Co-authored-by: Eric Leonardis <[email protected]> * Set `split_by_inds`, `test_labels`, and `validation_labels` to default (GUI) (#1331) * Allow returning PAF graph during low level inference (#1329) * allow returning the paf graph during low level inference * reformatted with black * Fix `SingleImageVideo` caching (#1330) * Set `SingleImageVideo.caching` as a class attribute * Modify tests for `SingleImageVideo.caching` * Add caching as a preference and menu checkbox * Test `SingleImageVideo.toggle_caching` * Remove GUI elements for `SingleImageVideo.CACHING` * Remove remaining prefs for `SingleImageVideo.CACHING` * Add depreciated comment * Clean-up * Update comments * Bump to 1.3.1 (#1335) * Bump to 1.3.1 * Test build to dev label * Update environment creation (#1366) * First 'working' env for 1.3.1, no GPU... * First working 1.3.1 w/gpu * Sorry, this is the first gpu working env * Fix `imgstore` version-dependent bug * Build and entry points work, but pip packages not installed * Add default channels in condarc.yaml * Rename environment.yaml to .yml * Working build no gpu (documented) * Env working w/gpu using tensorflow from pypi * Working build with GPU! And pip dep * Attempt to fix cannot find wheel ~= 0.35 issue * Run constrain everything * Use minimal conda req for install_requires, inc build number to get it working * Ubuntu build and environments working * Env creation working on M2 * Build and env working on windows (again) * Apple silicon (M2) build working * Pip package working (M2) * Exclude tests and docs from pypi wheel * Add comments to requirements * Get ready for manual build * Update os images, trigger dev build * Retry manual build win and mac * Retry mac manual build (to upload) * Require latest pynwb, remove setuptools * Remove old mac environment * Add twine as a build dependency * Add comments to manual build * Update build.yml * Rename "apple_silicon" to "mac" * Update installation docs (#1365) * Update installation docs * Trigger website build * Update quick install and build docs * Add Mambaforge links * Remove comment about experimental apple silicon support Co-authored-by: Talmo Pereira <[email protected]> * Fix minor typo * Change installation docs to reference universal mac env --------- Co-authored-by: Talmo Pereira <[email protected]> * More flexible with python version ~=3.7 * Pin py3.7.12 for host and run (good on win) * Add comments for why python ~=3.7 * Update ci workflow (#1371) * Update CI workflow to include mac * Trigger CI workflow * Remove verbose? python version * Migrate to micromamba * Explicitly state environment name * Remove environment chaching (for now) * Use different environment file for mac * Use correct syntax * Add `env_hash` and `bash -l {0}` * Remove env_file * Try different nested variable call via format * Use correct syntax * Update env file reference AS -> mac * Different path to environment file * Checkout repo * Use default shells * Remove unused comments * Fix caching attempt by changing caching key * Remove environment caching * Increase python in no_cuda to 3.7.17 * Less restrictive with python ~3.7 version * More direct installation docs 🤞 * Increase build numbers for develop branch build --------- Co-authored-by: Talmo Pereira <[email protected]> --------- Co-authored-by: Talmo Pereira <[email protected]> Co-authored-by: Eric Leonardis <[email protected]> Co-authored-by: Eric Leonardis <[email protected]> Co-authored-by: Caleb Weinreb <[email protected]>
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Description
Update runners for Windows and Ubuntu. Add runner for MacOS. Migrate to micromamba.
Types of changes
Does this address any currently open issues?
[list open issues here]
Outside contributors checklist
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