Feature/sbra 360 training on r2 combustion by rmslm · Pull Request #15 · AI4SIM/model-collection

rmslm · 2022-03-12T09:13:09Z

couple of refactoring R2 and cnf for gnns
Create symbolic links to data where ever the data are on Atos clusters to avoid duplicating large data
config files can take the link of the data as parameter

github-actions · 2022-03-12T09:15:01Z

Coverage report for weather_forecast/gwd/ use-case

File	Coverage		Missing
All files	`94%`	✅
data.py	`98%`	✅	`157`
models.py	`89%`	✅	`37-40` `90` `99`
trainer.py	`88%`	✅	`75-76` `80`

Minimum allowed coverage is 80%

Generated by 🐒 cobertura-action against 0de4a87

github-actions · 2022-03-12T09:16:03Z

Coverage report for combustion/gnns/ use-case

File	Coverage		Missing
All files	`80%`	✅
config.py	`66%`	❌	`74-75` `78-82` `87-92` `97-104`
data.py	`79%`	❌	`116-143` `174` `229` `276` `287`
models.py	`68%`	❌	`85` `116-131` `156-160` `210-214` `234-238`
plotters.py	`98%`	✅	`55-56`
trainer.py	`76%`	❌	`70-75` `79-80`

Minimum allowed coverage is 80%

Generated by 🐒 cobertura-action against 0de4a87

A669015 · 2022-03-17T16:18:10Z

There is a pycache file that should not be pushed.

A669015 · 2022-03-17T16:20:13Z

combustion/gnns/configs/default.yaml

-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-fit:


Is the UC no more functional on this file ?

A669015 · 2022-03-17T16:21:43Z

combustion/gnns/data/filenames.yaml

-# See the License for the specific language governing permissions and
-# limitations under the License.
-
- DNS1_00116000.h5


Is the UC no more functional on these data ?
Could we support the both dataset ? Maybe having several filenames.yaml files ?

i agree. both should coexist.

alxyok

combustion/pycache/init.cpython-38.pyc should also be removed?

alxyok · 2022-03-21T16:50:34Z

combustion/gnns/configs/gat.yaml

            num_workers: 0
-            y_normalizer : 342.553
+            y_normalizer: 3295.4
+            origin_path: '/wksp/data/raise/R2_flame/combustiondatabase/R2-filtered/R2-data' 


is this system-dependent?

The config file are always system-dependent IMHO since they are an extension of the CLI... they are logged in git only for educational purpose.

i don't agree. the rest of the arguments from those files can be run anywhere with no changes. not that one.
i don't think origin_path should be in the config files, the logic should be pulled out from the main flow

alxyok · 2022-03-21T16:55:15Z

combustion/gnns/data.py

        Creates the main Dataset and splits the train, test and validation Datasets from the main
        Dataset. Currently the repartition is respectively, 80%, 10% and 10% from the main Dataset
-        size.
+        size. Creates symbolic links from origin data.


this is an optional preprocessing step.
it should be run outside the main logic from a bash script maybe.

I agree with that, we should find a way to keep that out of the core code, it's config-oriented.

alxyok · 2022-03-21T16:55:52Z

combustion/gnns/data.py

+        self.local_raw_data = os.path.join(data_path, 'raw')
+        if os.path.exists(self.local_raw_data):
+
+            try :


this should be mv outside the main execution flow

alxyok · 2022-03-21T16:57:12Z

combustion/gnns/data/filenames.yaml

-# See the License for the specific language governing permissions and
-# limitations under the License.
-
- DNS1_00116000.h5


i agree. both should coexist.

leonicoletti · 2022-03-25T10:57:13Z

combustion/gnns/data.py

+
+
+
+class R2Process(CombustionDataset) :


I would rather call it R2Dataset (I think the name should rather denote the fact that it's a dataset)

leonicoletti · 2022-03-25T10:57:33Z

combustion/gnns/data.py

+

-    def get(self, idx: int) -> pyg.data.Data:
+class CnfProcess(CombustionDataset) :


leonicoletti

I like the subclassing of CombustionDataset.

alxyok · 2022-03-28T08:46:20Z

combustion/gnns/configs/gat.yaml

            num_workers: 0
-            y_normalizer : 342.553
+            y_normalizer: 3295.4
+            origin_path: '/wksp/data/raise/R2_flame/combustiondatabase/R2-filtered/R2-data' 


i don't agree. the rest of the arguments from those files can be run anywhere with no changes. not that one.
i don't think origin_path should be in the config files, the logic should be pulled out from the main flow

alxyok · 2022-03-28T08:46:46Z

combustion/gnns/configs/gin.yaml

        accelerator: "gpu"
-        devices:
-            - 0
+        callbacks:


good idea indeed

alxyok · 2022-03-28T08:49:43Z

combustion/gnns/data.py


            with h5py.File(raw_path, 'r') as file:
-                c = file["/filt_8"][:]
+                c = file["/c_filt"][:]


Suggested change

c = file["/c_filt"][:]

c = file["/c_filt"][:]

sigma = file["/c_grad_filt"][:]

if self.y_normalizer:

sigma /= self.y_normalizer

github-actions · 2022-03-28T10:33:22Z

Coverage report for combustion/unets/ use-case

File	Coverage		Missing
All files	`93%`	✅
data.py	`93%`	✅	`61` `72` `74` `113` `116`
models.py	`87%`	✅	`41-42` `45` `48`
trainer.py	`77%`	❌	`59-61` `65-66` `69`

Minimum allowed coverage is 80%

Generated by 🐒 cobertura-action against 0de4a87

* Adding pangu weather (#1) * re-add pangu-weather after branch cleanup * reduced spatial resolution for tests * fixed isort issue * fixed black issue * fixed accelerator issue * added .coveragerc and .gitignore * removed unnecessary requirements, and testing github repository name * changed pangu-weather to global-emulation, updated requirement with pip freeze, added global-emulation to images-ci-cd matrix * changed image ci cd to only push the Docker images in model-collection * fixed requirements, removed weatherlearn mentions from readme, renamed pangu into panguweather * added nox back in requirements * fixed panguweather import, removed unused imports * removed debug test from images-ci-cd, deleted config_pangu_micro, updated DropPath to use timm directly, removed unused models (MockPanguModel and CustomPanguModel), removed generate_3d_attention_mask_old and its associated test, aligned trainer.py with the others in weather-forecast * removed unused Dockerfiles * added git to dockerfile * made the init of transformer_module more pythonic * renamed global emulation to nwp emulation * renamed global emulation to nwp emulation in the cicd * [SBRA-837] Add mypy automatic checking to CI/CD (#4) * Add a common mypy.ini file * Add specific mypy config for pangu, Add mypy session to nox * add mypy_cache to gitignore * Add mypy session to ci/cd * Improve PanguWeather type hints * fix pangu lint * Add mypy to gravity-wave-drag * fix test_utils import * fix unit test on data * Add mypy checks to ecrad-3d-correction * Add mypy checks to combustion unet * Add mypy check to combustion gnn * fix format * fix unit test wrt previous code modification * [SBRA-870] Polish code for open access release (#5) * fix time_horizon error print * fix typo * fix casual comments * remove useless comments * improve comment * improve print info --------- Co-authored-by: mikael jacquemont <mikael.jacquemont@eviden.com> * fix format after black update (#6) * Bump mlflow from 2.17.2 to 2.20.3 in /weather-forecast/nwp-emulation/panguweather in the pip group across 1 directory (#3) * Bump mlflow Bumps the pip group with 1 update in the /weather-forecast/nwp-emulation/panguweather directory: [mlflow](https://github.com/mlflow/mlflow). Updates `mlflow` from 2.17.2 to 2.20.3 - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](mlflow/mlflow@v2.17.2...v2.20.3) --- updated-dependencies: - dependency-name: mlflow dependency-version: 2.20.3 dependency-type: direct:production dependency-group: pip ... Signed-off-by: dependabot[bot] <support@github.com> * Apply black * Fix mlflow-skinny version * Revert "Fix mlflow-skinny version" This reverts commit 1bf04081ea5f324e91993f9ac24cf718dac5a6f7. * Revert "Apply black" This reverts commit 5c1ab8075cb29dfa13694168f3048dff1b8d62f5. * Fix mlflow-skinny version --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mikaël Jacquemont <mikael.jacquemont@atos.net> * Refactor projects install (#8) * use uv instead of pip and python * Let uv manage python and dependencies * fix python version for all nox sessions * fix find wheel version * remove useless uv sync * update pangu * update cnns * update ecrad unets * update cnf unets * update gnns * update ci/cd workflow * update docker build * update doc * use large runner for docker image workflow * add dependabot.yml file * Bump the uv group across 4 directories with 1 update (#9) * Bump the uv group across 4 directories with 1 update Bumps the uv group with 1 update in the /weather-forecast/nwp-emulation/panguweather directory: [torch](https://github.com/pytorch/pytorch). Bumps the uv group with 1 update in the /weather-forecast/gravity-wave-drag/cnns directory: [torch](https://github.com/pytorch/pytorch). Bumps the uv group with 1 update in the /weather-forecast/ecrad-3d-correction/unets directory: [torch](https://github.com/pytorch/pytorch). Bumps the uv group with 1 update in the /reactive-flows/cnf-combustion/unets directory: [torch](https://github.com/pytorch/pytorch). Updates `torch` from 2.6.0 to 2.8.0 - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v2.6.0...v2.8.0) Updates `torch` from 2.6.0 to 2.8.0 - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v2.6.0...v2.8.0) Updates `torch` from 2.6.0 to 2.8.0 - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v2.6.0...v2.8.0) Updates `torch` from 2.6.0 to 2.8.0 - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v2.6.0...v2.8.0) --- updated-dependencies: - dependency-name: torch dependency-version: 2.8.0 dependency-type: direct:production dependency-group: uv - dependency-name: torch dependency-version: 2.8.0 dependency-type: direct:production dependency-group: uv - dependency-name: torch dependency-version: 2.8.0 dependency-type: direct:production dependency-group: uv - dependency-name: torch dependency-version: 2.8.0 dependency-type: direct:production dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> * fix mypy issue * replacing float casting by item() --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: VINCENT, LIONEL <lionel.vincent.dm@atos.net> Co-authored-by: mikael10j <mikael.jacquemont@eviden.com> * improve install using explicit index and find-link for torch and pyg (#10) * Bump the uv group across 5 directories with 8 updates (#11) Bumps the uv group with 8 updates in the /reactive-flows/cnf-combustion/gnns directory: | Package | From | To | | --- | --- | --- | | [certifi](https://github.com/certifi/python-certifi) | `2022.12.7` | `2024.7.4` | | [filelock](https://github.com/tox-dev/py-filelock) | `3.20.0` | `3.20.3` | | [idna](https://github.com/kjd/idna) | `3.4` | `3.7` | | [pillow](https://github.com/python-pillow/Pillow) | `12.0.0` | `12.1.1` | | [requests](https://github.com/psf/requests) | `2.28.1` | `2.32.4` | | [setuptools](https://github.com/pypa/setuptools) | `70.2.0` | `78.1.1` | | [urllib3](https://github.com/urllib3/urllib3) | `1.26.13` | `2.6.3` | | [werkzeug](https://github.com/pallets/werkzeug) | `3.1.5` | `3.1.6` | Bumps the uv group with 1 update in the /reactive-flows/cnf-combustion/unets directory: [werkzeug](https://github.com/pallets/werkzeug). Bumps the uv group with 1 update in the /weather-forecast/ecrad-3d-correction/unets directory: [werkzeug](https://github.com/pallets/werkzeug). Bumps the uv group with 4 updates in the /weather-forecast/gravity-wave-drag/cnns directory: [filelock](https://github.com/tox-dev/py-filelock), [idna](https://github.com/kjd/idna), [setuptools](https://github.com/pypa/setuptools) and [werkzeug](https://github.com/pallets/werkzeug). Bumps the uv group with 5 updates in the /weather-forecast/nwp-emulation/panguweather directory: | Package | From | To | | --- | --- | --- | | [certifi](https://github.com/certifi/python-certifi) | `2022.12.7` | `2024.7.4` | | [filelock](https://github.com/tox-dev/py-filelock) | `3.20.0` | `3.20.3` | | [idna](https://github.com/kjd/idna) | `3.4` | `3.7` | | [pillow](https://github.com/python-pillow/Pillow) | `12.0.0` | `12.1.1` | | [setuptools](https://github.com/pypa/setuptools) | `70.2.0` | `78.1.1` | Updates `certifi` from 2022.12.7 to 2024.7.4 - [Commits](certifi/python-certifi@2022.12.07...2024.07.04) Updates `filelock` from 3.20.0 to 3.20.3 - [Release notes](https://github.com/tox-dev/py-filelock/releases) - [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst) - [Commits](tox-dev/filelock@3.20.0...3.20.3) Updates `idna` from 3.4 to 3.7 - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.4...v3.7) Updates `pillow` from 12.0.0 to 12.1.1 - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.0.0...12.1.1) Updates `requests` from 2.28.1 to 2.32.4 - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.28.1...v2.32.4) Updates `setuptools` from 70.2.0 to 78.1.1 - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v70.2.0...v78.1.1) Updates `urllib3` from 1.26.13 to 2.6.3 - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.13...2.6.3) Updates `werkzeug` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.1.5...3.1.6) Updates `werkzeug` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.1.5...3.1.6) Updates `werkzeug` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.1.5...3.1.6) Updates `filelock` from 3.20.0 to 3.20.3 - [Release notes](https://github.com/tox-dev/py-filelock/releases) - [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst) - [Commits](tox-dev/filelock@3.20.0...3.20.3) Updates `idna` from 3.4 to 3.7 - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.4...v3.7) Updates `setuptools` from 70.2.0 to 78.1.1 - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v70.2.0...v78.1.1) Updates `werkzeug` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.1.5...3.1.6) Updates `certifi` from 2022.12.7 to 2024.7.4 - [Commits](certifi/python-certifi@2022.12.07...2024.07.04) Updates `filelock` from 3.20.0 to 3.20.3 - [Release notes](https://github.com/tox-dev/py-filelock/releases) - [Changelog](https://github.com/tox-dev/filelock/blob/main/docs/changelog.rst) - [Commits](tox-dev/filelock@3.20.0...3.20.3) Updates `idna` from 3.4 to 3.7 - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](kjd/idna@v3.4...v3.7) Updates `pillow` from 12.0.0 to 12.1.1 - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.0.0...12.1.1) Updates `setuptools` from 70.2.0 to 78.1.1 - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v70.2.0...v78.1.1) --- updated-dependencies: - dependency-name: certifi dependency-version: 2024.7.4 dependency-type: indirect dependency-group: uv - dependency-name: filelock dependency-version: 3.20.3 dependency-type: indirect dependency-group: uv - dependency-name: idna dependency-version: '3.7' dependency-type: indirect dependency-group: uv - dependency-name: pillow dependency-version: 12.1.1 dependency-type: indirect dependency-group: uv - dependency-name: requests dependency-version: 2.32.4 dependency-type: indirect dependency-group: uv - dependency-name: setuptools dependency-version: 78.1.1 dependency-type: indirect dependency-group: uv - dependency-name: urllib3 dependency-version: 2.6.3 dependency-type: indirect dependency-group: uv - dependency-name: werkzeug dependency-version: 3.1.6 dependency-type: indirect dependency-group: uv - dependency-name: werkzeug dependency-version: 3.1.6 dependency-type: indirect dependency-group: uv - dependency-name: werkzeug dependency-version: 3.1.6 dependency-type: indirect dependency-group: uv - dependency-name: filelock dependency-version: 3.20.3 dependency-type: indirect dependency-group: uv - dependency-name: idna dependency-version: '3.7' dependency-type: indirect dependency-group: uv - dependency-name: setuptools dependency-version: 78.1.1 dependency-type: indirect dependency-group: uv - dependency-name: werkzeug dependency-version: 3.1.6 dependency-type: indirect dependency-group: uv - dependency-name: certifi dependency-version: 2024.7.4 dependency-type: indirect dependency-group: uv - dependency-name: filelock dependency-version: 3.20.3 dependency-type: indirect dependency-group: uv - dependency-name: idna dependency-version: '3.7' dependency-type: indirect dependency-group: uv - dependency-name: pillow dependency-version: 12.1.1 dependency-type: indirect dependency-group: uv - dependency-name: setuptools dependency-version: 78.1.1 dependency-type: indirect dependency-group: uv ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix README (#12) * fix README * Add missing line Co-authored-by: Mikaël Jacquemont <mikael.jacquemont@atos.net> --------- Co-authored-by: Mikaël Jacquemont <mikael.jacquemont@atos.net> * add workflow to automate PR proposal in public when merging in private (#13) * fix branch name (#14) * fix dependabot.yaml (#15) * Automate PR proposal in public - fix credentials (#16) * fix job name * Add branch and PR creation --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: MarcMichouxEviden <106808701+MarcMichouxAtos@users.noreply.github.com> Co-authored-by: Mikaël Jacquemont <mikael.jacquemont@atos.net> Co-authored-by: mikael jacquemont <mikael.jacquemont@eviden.com> Co-authored-by: Lionel VINCENT <97742788+A669015@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: VINCENT, LIONEL <lionel.vincent.dm@atos.net>

A669015 reviewed Mar 17, 2022

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alxyok suggested changes Mar 21, 2022

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leonicoletti reviewed Mar 25, 2022

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combustion/gnns/data.py Outdated

def get(self, idx: int) -> pyg.data.Data:

class CnfProcess(CombustionDataset) :

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leonicoletti Mar 25, 2022

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ditto

leonicoletti approved these changes Mar 25, 2022

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alxyok suggested changes Mar 28, 2022

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rmslm added 2 commits March 28, 2022 10:29

[SBRA-360] Generiliza R2 and Cnf use case

d6440d8

[SBRA-360] Generiliza R2 and Cnf use case

063249c

rmslm force-pushed the feature/SBRA-360-training-on-R2-combustion branch from bf8547d to 063249c Compare March 28, 2022 10:31

fix tests

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alxyok approved these changes Apr 6, 2022

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rmslm added 3 commits April 6, 2022 15:51

Merge branch 'main' into feature/SBRA-360-training-on-R2-combustion

2486a94

re-edit test file after PR

7cd935e

fix bug after PR

0de4a87

rmslm merged commit 531185a into main Apr 8, 2022

rmslm deleted the feature/SBRA-360-training-on-R2-combustion branch April 8, 2022 08:06

A669015 mentioned this pull request Apr 13, 2022

Fix bad conflict resolution in GNN #22

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ai4sim-pr-app bot pushed a commit that referenced this pull request Feb 27, 2026

fix dependabot.yaml (#15)

893ecdc

github-actions bot pushed a commit that referenced this pull request Mar 2, 2026

fix dependabot.yaml (#15)

4536f4d



		def get(self, idx: int) -> pyg.data.Data:
		class CnfProcess(CombustionDataset) :

-                c = file["/c_filt"][:]
+                c = file["/c_filt"][:]
+                sigma = file["/c_grad_filt"][:]
+                if self.y_normalizer:
+                    sigma /= self.y_normalizer

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github-actions bot commented Mar 28, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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github-actions bot commented Mar 12, 2022 •

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github-actions bot commented Mar 12, 2022 •

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github-actions bot commented Mar 28, 2022 •

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