From e47ef1765738dce319f22051155a495b8d4dff93 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Sun, 1 Oct 2023 12:02:15 -0400 Subject: [PATCH 01/33] hello world --- training/training/core/dl_model.py | 1 + 1 file changed, 1 insertion(+) diff --git a/training/training/core/dl_model.py b/training/training/core/dl_model.py index d35d0ff17..e347b81f8 100644 --- a/training/training/core/dl_model.py +++ b/training/training/core/dl_model.py @@ -41,6 +41,7 @@ def fromLayerParamsList(cls, layer_params_list: list[LayerParams]): return cls(layer_list) def build_model(self, layer_list): + print ("Hello World") model = nn.Sequential() ctr = 1 for layer in layer_list: From 68599780eca8adf645149cdc84d01a3e5a6bf4fe Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Sun, 1 Oct 2023 12:42:34 -0400 Subject: [PATCH 02/33] old changes new branch --- training/poetry.lock | 20 ++++++- training/pyproject.toml | 1 + training/pytest.ini | 2 + training/tests/test_imports.py | 6 ++ training/tests/test_loss_function.py | 60 +++++++++++++++++++ training/tests/test_model.py | 33 ++++++++++ training/training/core/dl_model.py | 4 +- .../routes/datasets/default/__init__.py | 5 -- training/training/routes/tabular/__init__.py | 4 -- training/training/urls.py | 8 +-- 10 files changed, 126 insertions(+), 17 deletions(-) create mode 100644 training/pytest.ini create mode 100644 training/tests/test_imports.py create mode 100644 training/tests/test_loss_function.py create mode 100644 training/tests/test_model.py diff --git a/training/poetry.lock b/training/poetry.lock index 978079114..60b4a5fa0 100644 --- a/training/poetry.lock +++ b/training/poetry.lock @@ -1561,6 +1561,24 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +[[package]] +name = "pytest-django" +version = "4.5.2" +description = "A Django plugin for pytest." +optional = false +python-versions = ">=3.5" +files = [ + {file = "pytest-django-4.5.2.tar.gz", hash = "sha256:d9076f759bb7c36939dbdd5ae6633c18edfc2902d1a69fdbefd2426b970ce6c2"}, + {file = "pytest_django-4.5.2-py3-none-any.whl", hash = "sha256:c60834861933773109334fe5a53e83d1ef4828f2203a1d6a0fa9972f4f75ab3e"}, +] + +[package.dependencies] +pytest = ">=5.4.0" + +[package.extras] +docs = ["sphinx", "sphinx-rtd-theme"] +testing = ["Django", "django-configurations (>=2.0)"] + [[package]] name = "python-dateutil" version = "2.8.2" @@ -2018,4 +2036,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.10" -content-hash = "d8c76026a0a5692cb21fd72814d180c6aa36e6d00b43eefc29e5f6f281d57045" +content-hash = "d3e63638e340d09084cc4504004769b7dc6b0ad65e08b9c0b8dd02548b274428" diff --git a/training/pyproject.toml b/training/pyproject.toml index f20ed5b4b..b3cbe110f 100644 --- a/training/pyproject.toml +++ b/training/pyproject.toml @@ -23,6 +23,7 @@ django-cors-headers = "^4.2.0" pytest = "^7.4.0" ggshield = "^1.18.0" moto = "^4.1.14" +pytest-django = "^4.5.2" [build-system] requires = ["poetry-core"] diff --git a/training/pytest.ini b/training/pytest.ini new file mode 100644 index 000000000..a8b7a9643 --- /dev/null +++ b/training/pytest.ini @@ -0,0 +1,2 @@ +[pytest] +DJANGO_SETTINGS_MODULE = training.settings \ No newline at end of file diff --git a/training/tests/test_imports.py b/training/tests/test_imports.py new file mode 100644 index 000000000..cddba8b47 --- /dev/null +++ b/training/tests/test_imports.py @@ -0,0 +1,6 @@ +def test_all_imports(): + import training.core.dataset + import training.core.criterion + import training.core.optimizer + import training.core.dl_model + import training.core.trainer diff --git a/training/tests/test_loss_function.py b/training/tests/test_loss_function.py new file mode 100644 index 000000000..bcd1f09d2 --- /dev/null +++ b/training/tests/test_loss_function.py @@ -0,0 +1,60 @@ +import pytest +import torch +import torch.nn as nn +from training.core.criterion import getCriterionHandler + + +""" +Unit tests to check that the loss function is being computed correctly +""" + + +# initialize some tensors +zero_tensor = torch.zeros(10, 1, 1) +one_tensor = torch.ones(10, 1, 1) +tensor_vstack_one = torch.vstack( + [torch.tensor([[2.5], [56.245], [2342.68967]]), torch.tensor([[3], [4], [5]])] +).reshape((6, 1, 1)) +tensor_vstack_two = torch.vstack( + [torch.tensor([[5646456], [634767], [37647346]]), torch.tensor([[6], [7], [8]])] +).reshape((6, 1, 1)) + +def compute_loss(loss_function_name, output, labels): + loss_function = getCriterionHandler(loss_function_name) + return loss_function.compute_loss(output, labels) + +@pytest.mark.parametrize( + "output, labels, expected_number", + [ + (zero_tensor, one_tensor, 1.0), + (tensor_vstack_one, tensor_vstack_two, 7321426), + ], +) +def test_l1_loss_computation_correct(output, labels, expected_number): + loss_function_name = "L1LOSS" + computed_loss = compute_loss(loss_function_name, output, labels) + assert pytest.approx(expected_number) == computed_loss + +@pytest.mark.parametrize( + "output, labels, expected_number", + [ + (zero_tensor, one_tensor, 1.0), + (tensor_vstack_one, tensor_vstack_two, 15543340), + ], +) +def test_mse_loss_computation_correct(output, labels, expected_number): + loss_function_name = "MSELOSS" + loss_function = getCriterionHandler("MSELOSS") + computed_loss = compute_loss(loss_function_name, output, labels) + print(torch.sqrt(computed_loss)) + assert pytest.approx(expected_number) == torch.sqrt(computed_loss) + + +@pytest.mark.parametrize( + "output, labels, expected_number", + [(zero_tensor.reshape((10, 1)), one_tensor.reshape(10), 100)], +) +def test_bce_loss_computation_correct(output, labels, expected_number): + loss_function_name = "BCELOSS" + computed_loss = compute_loss(loss_function_name, output, labels) + assert pytest.approx(expected_number) == computed_loss \ No newline at end of file diff --git a/training/tests/test_model.py b/training/tests/test_model.py new file mode 100644 index 000000000..fcc99c8bd --- /dev/null +++ b/training/tests/test_model.py @@ -0,0 +1,33 @@ +import pytest +import torch.nn as nn +from torch.autograd import Variable +from training.core.dl_model import DLModel + + +@pytest.mark.parametrize( + "input_list", + [ + ([nn.Linear(10, 5), nn.Linear(5, 3)]), + ([nn.Linear(0, 0), nn.Linear(0, 0)]), + ([nn.Linear(100, 50), nn.Linear(5, 3)]), + ], +) +def test_dlmodel(input_list): + print("input_list: " + str(input_list) + " is of type " + str(type(input_list))) + my_model = DLModel(input_list) + print("my_model: " + str(my_model) + " is of type " + str(type(my_model))) + print( + "[module for module in my_model.model.modules() if not isinstance(module, nn.Sequential)]: " + + str( + [ + module + for module in my_model.model.modules() + if not isinstance(module, nn.Sequential) + ] + ) + ) + assert [ + module + for module in my_model.model.modules() + if not isinstance(module, nn.Sequential) + ] == input_list \ No newline at end of file diff --git a/training/training/core/dl_model.py b/training/training/core/dl_model.py index e347b81f8..21e95afaa 100644 --- a/training/training/core/dl_model.py +++ b/training/training/core/dl_model.py @@ -1,8 +1,6 @@ from typing import Any, Callable -from ninja import Schema import torch import torch.nn as nn -from typing import TYPE_CHECKING from training.routes.tabular.schemas import LayerParams @@ -50,5 +48,5 @@ def build_model(self, layer_list): return model def forward(self, x: torch.Tensor): - pred = self.model(x) # apply model on input x + pred = self.model(x) return pred diff --git a/training/training/routes/datasets/default/__init__.py b/training/training/routes/datasets/default/__init__.py index 2a6f5e11b..e69de29bb 100644 --- a/training/training/routes/datasets/default/__init__.py +++ b/training/training/routes/datasets/default/__init__.py @@ -1,5 +0,0 @@ -from training.routes.datasets.default.columns import router - - -def get_default_datasets_router(): - return router diff --git a/training/training/routes/tabular/__init__.py b/training/training/routes/tabular/__init__.py index 25bffee05..8b1378917 100644 --- a/training/training/routes/tabular/__init__.py +++ b/training/training/routes/tabular/__init__.py @@ -1,5 +1 @@ -from training.routes.tabular.tabular import router - -def get_tabular_router(): - return router diff --git a/training/training/urls.py b/training/training/urls.py index c79e13107..f165df260 100644 --- a/training/training/urls.py +++ b/training/training/urls.py @@ -19,8 +19,8 @@ from django.http import HttpRequest from django.urls import path from ninja import NinjaAPI, Schema -from training.routes.datasets.default import get_default_datasets_router -from training.routes.tabular import get_tabular_router +from training.routes.datasets.default.columns import router as default_dataset_router +from training.routes.tabular.tabular import router as tabular_router api = NinjaAPI() @@ -30,8 +30,8 @@ def test(request: HttpRequest): return 200, {"result": "200 Backend surface test successful"} -api.add_router("/datasets/default/", get_default_datasets_router()) -api.add_router("/tabular", get_tabular_router()) +api.add_router("/datasets/default/", default_dataset_router) +api.add_router("/tabular", tabular_router) urlpatterns = [ path("admin/", admin.site.urls), From 9910b26cd95cc95db0bd3523690ca68ac561e534 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Sun, 1 Oct 2023 12:50:31 -0400 Subject: [PATCH 03/33] update ubuntu --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index a7749a3e1..7f7fb95c6 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -12,7 +12,7 @@ on: jobs: lint: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest steps: #---------------------------------------------- # check-out repo and set-up mamba env From aad5576029cf2c0e16cf4f74301437d377768994 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Sun, 1 Oct 2023 12:56:58 -0400 Subject: [PATCH 04/33] poetry lock --- training/poetry.lock | 918 ++++++++++++++++++++++--------------------- 1 file changed, 461 insertions(+), 457 deletions(-) diff --git a/training/poetry.lock b/training/poetry.lock index 60b4a5fa0..e42d452e6 100644 --- a/training/poetry.lock +++ b/training/poetry.lock @@ -30,32 +30,32 @@ tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"] [[package]] name = "boto3" -version = "1.28.15" +version = "1.28.57" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.15-py3-none-any.whl", hash = "sha256:84b7952858e9319968b0348d9894a91a6bb5f31e81a45c68044d040a12362abe"}, - {file = "boto3-1.28.15.tar.gz", hash = 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hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"}, ] [[package]] @@ -1987,13 +1991,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.24.3" +version = "20.24.5" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.24.3-py3-none-any.whl", hash = "sha256:95a6e9398b4967fbcb5fef2acec5efaf9aa4972049d9ae41f95e0972a683fd02"}, - {file = "virtualenv-20.24.3.tar.gz", hash = "sha256:e5c3b4ce817b0b328af041506a2a299418c98747c4b1e68cb7527e74ced23efc"}, + {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"}, + {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"}, ] [package.dependencies] @@ -2002,18 +2006,18 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<4" [package.extras] -docs = ["furo (>=2023.5.20)", 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"sha256:98c774df2f91b05550078891dee5f0eb0cb797a522c757a2452b9cee5b202330"}, + {file = "werkzeug-3.0.0-py3-none-any.whl", hash = "sha256:cbb2600f7eabe51dbc0502f58be0b3e1b96b893b05695ea2b35b43d4de2d9962"}, + {file = "werkzeug-3.0.0.tar.gz", hash = "sha256:3ffff4dcc32db52ef3cc94dff3000a3c2846890f3a5a51800a27b909c5e770f0"}, ] [package.dependencies] From 68adebf809e59993cae671fe89efcd1bbf114768 Mon Sep 17 00:00:00 2001 From: prishavall Date: Sun, 1 Oct 2023 16:57:40 +0000 Subject: [PATCH 05/33] :art: Format Python code with psf/black --- training/tests/test_loss_function.py | 7 +++++-- training/tests/test_model.py | 2 +- training/training/core/dl_model.py | 4 ++-- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/training/tests/test_loss_function.py b/training/tests/test_loss_function.py index bcd1f09d2..bee1ddc6c 100644 --- a/training/tests/test_loss_function.py +++ b/training/tests/test_loss_function.py @@ -19,10 +19,12 @@ [torch.tensor([[5646456], [634767], [37647346]]), torch.tensor([[6], [7], [8]])] ).reshape((6, 1, 1)) + def compute_loss(loss_function_name, output, labels): loss_function = getCriterionHandler(loss_function_name) return loss_function.compute_loss(output, labels) - + + @pytest.mark.parametrize( "output, labels, expected_number", [ @@ -35,6 +37,7 @@ def test_l1_loss_computation_correct(output, labels, expected_number): computed_loss = compute_loss(loss_function_name, output, labels) assert pytest.approx(expected_number) == computed_loss + @pytest.mark.parametrize( "output, labels, expected_number", [ @@ -57,4 +60,4 @@ def test_mse_loss_computation_correct(output, labels, expected_number): def test_bce_loss_computation_correct(output, labels, expected_number): loss_function_name = "BCELOSS" computed_loss = compute_loss(loss_function_name, output, labels) - assert pytest.approx(expected_number) == computed_loss \ No newline at end of file + assert pytest.approx(expected_number) == computed_loss diff --git a/training/tests/test_model.py b/training/tests/test_model.py index fcc99c8bd..c1a4a098d 100644 --- a/training/tests/test_model.py +++ b/training/tests/test_model.py @@ -30,4 +30,4 @@ def test_dlmodel(input_list): module for module in my_model.model.modules() if not isinstance(module, nn.Sequential) - ] == input_list \ No newline at end of file + ] == input_list diff --git a/training/training/core/dl_model.py b/training/training/core/dl_model.py index 21e95afaa..63c45ad87 100644 --- a/training/training/core/dl_model.py +++ b/training/training/core/dl_model.py @@ -39,7 +39,7 @@ def fromLayerParamsList(cls, layer_params_list: list[LayerParams]): return cls(layer_list) def build_model(self, layer_list): - print ("Hello World") + print("Hello World") model = nn.Sequential() ctr = 1 for layer in layer_list: @@ -48,5 +48,5 @@ def build_model(self, layer_list): return model def forward(self, x: torch.Tensor): - pred = self.model(x) + pred = self.model(x) return pred From 49c78d18b0d738b6ed6ff4f5a93de7bb92f38aca Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 12:39:09 -0400 Subject: [PATCH 06/33] tmate debug --- .github/workflows/backend.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 7f7fb95c6..abf5b276c 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -19,6 +19,8 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 + - name: Setup tmate session + uses: mxschmitt/action-tmate@v3 - uses: mamba-org/setup-micromamba@v1 with: From a2a08e49a9e0e864f56acd30238cb178b2ca6255 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 13:30:09 -0400 Subject: [PATCH 07/33] miniforge shell alt action --- .github/workflows/backend.yml | 27 ++++++++++++++++++--------- dlp-cli | 2 +- 2 files changed, 19 insertions(+), 10 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index abf5b276c..b74548d7b 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -19,17 +19,26 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 - - name: Setup tmate session - uses: mxschmitt/action-tmate@v3 - - - uses: mamba-org/setup-micromamba@v1 + # - name: Setup tmate session + # uses: mxschmitt/action-tmate@v3 + + - uses: conda-incubator/setup-miniconda@v2 with: - micromamba-version: '1.4.5-0' environment-file: training/environment.yml - init-shell: >- - bash - cache-environment: true - cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} + miniforge-version: latest + use-mamba: true + activate-environment: dlp + run: | + pwd + + # - uses: mamba-org/setup-micromamba@v1 + # with: + # micromamba-version: '1.4.5-0' + # environment-file: training/environment.yml + # init-shell: >- + # bash + # cache-environment: true + # cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} #---------------------------------------------- # load cached venv if cache exists diff --git a/dlp-cli b/dlp-cli index 2ed81dc17..ac534bab5 160000 --- a/dlp-cli +++ b/dlp-cli @@ -1 +1 @@ -Subproject commit 2ed81dc1703ae0eeab6417e0f1ac91aaf2dfc133 +Subproject commit ac534bab5e929e275f10db33778100a00b0c7cae From a3196adf8b8b996d1965b041db566e595a753502 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 13:31:43 -0400 Subject: [PATCH 08/33] indent --- .github/workflows/backend.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index b74548d7b..0854c6a1d 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -28,8 +28,8 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - run: | - pwd + run: | + pwd # - uses: mamba-org/setup-micromamba@v1 # with: From c433701d1dfadf52527bad1ead0a0513af7d4863 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 13:42:36 -0400 Subject: [PATCH 09/33] mamba miniforge3 shell --- .github/workflows/backend.yml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 0854c6a1d..9f1f9e025 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -28,8 +28,6 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - run: | - pwd # - uses: mamba-org/setup-micromamba@v1 # with: @@ -47,9 +45,16 @@ jobs: id: cached-poetry-dependencies uses: actions/cache@v3 with: - path: /home/runner/micromamba/envs/dlp/ + path: /usr/share/miniconda3/envs/dlp key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} restore-keys: training-venv-${{ runner.os }}- + # - name: Load cached venv + # id: cached-poetry-dependencies + # uses: actions/cache@v3 + # with: + # path: /home/runner/micromamba/envs/dlp/ + # key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} + # restore-keys: training-venv-${{ runner.os }}- #--------------------------------------------------- # install dependencies if cache does not exist @@ -58,7 +63,8 @@ jobs: - name: Install dependencies if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: pwd && cd training && poetry install --no-interaction --no-root && poetry env info -p - shell: micromamba-shell {0} + shell: bash -el {0} + #shell: micromamba-shell {0} #---------------------------------------------- # pyright static checker From 234dfff9395ca45f1180091dc5574f3c1755ad90 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 15:00:41 -0400 Subject: [PATCH 10/33] test job update --- .github/workflows/backend.yml | 38 ++++++++++++++++++++++++++--------- 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 9f1f9e025..04c6a171a 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -103,32 +103,49 @@ jobs: - name: Check out repository uses: actions/checkout@v3 - - uses: mamba-org/setup-micromamba@v1 + - uses: conda-incubator/setup-miniconda@v2 with: - micromamba-version: '1.4.5-0' environment-file: training/environment.yml - init-shell: >- - bash - cache-environment: true - cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} + miniforge-version: latest + use-mamba: true + activate-environment: dlp + + # - uses: mamba-org/setup-micromamba@v1 + # with: + # micromamba-version: '1.4.5-0' + # environment-file: training/environment.yml + # init-shell: >- + # bash + # cache-environment: true + # cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} #---------------------------------------------- # load cached venv if cache exists #---------------------------------------------- + - name: Load cached venv id: cached-poetry-dependencies uses: actions/cache@v3 with: - path: /home/runner/micromamba/envs/dlp/ + path: /usr/share/miniconda3/envs/dlp key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} restore-keys: training-venv-${{ runner.os }}- + + # - name: Load cached venv + # id: cached-poetry-dependencies + # uses: actions/cache@v3 + # with: + # path: /home/runner/micromamba/envs/dlp/ + # key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} + # restore-keys: training-venv-${{ runner.os }}- #---------------------------------------------- # install dependencies if cache does not exist #---------------------------------------------- - name: Install dependencies if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: cd training && poetry install --no-interaction --no-root - shell: micromamba-shell {0} + shell: bash -el {0} + #shell: micromamba-shell {0} #---------------------------------------------- # run test suite #---------------------------------------------- @@ -137,6 +154,7 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 - # cd training && pytest tests - shell: micromamba-shell {0} + cd training && pytest tests + shell: bash -el {0} + #shell: micromamba-shell {0} From 4df8afee5052851413712bc94684da8602286c2c Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 15:11:34 -0400 Subject: [PATCH 11/33] cache support for miniforge env --- .github/workflows/backend.yml | 35 +++++++++++++++++++++++++++++++++-- 1 file changed, 33 insertions(+), 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 04c6a171a..e0c9329ef 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -21,8 +21,20 @@ jobs: uses: actions/checkout@v3 # - name: Setup tmate session # uses: mxschmitt/action-tmate@v3 + + - name: Load Cached Mamba Env + id: cached-mamba-env + uses: actions/cache@v3 + with: + path: ${{ env.CONDA }}/envs + key: + mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} + restore-keys: mamba-env-${{ runner.os }}- + - - uses: conda-incubator/setup-miniconda@v2 + - name: Install Mamba Env + if: steps.cached-mamba-env.outputs.cache-hit != 'true' + uses: conda-incubator/setup-miniconda@v2 with: environment-file: training/environment.yml miniforge-version: latest @@ -102,13 +114,32 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 + + - name: Load Cached Mamba Env + id: cached-mamba-env + uses: actions/cache@v3 + with: + path: ${{ env.CONDA }}/envs + key: + mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} + restore-keys: mamba-env-${{ runner.os }}- + - - uses: conda-incubator/setup-miniconda@v2 + - name: Install Mamba Env + if: steps.cached-mamba-env.outputs.cache-hit != 'true' + uses: conda-incubator/setup-miniconda@v2 with: environment-file: training/environment.yml miniforge-version: latest use-mamba: true activate-environment: dlp + + # - uses: conda-incubator/setup-miniconda@v2 + # with: + # environment-file: training/environment.yml + # miniforge-version: latest + # use-mamba: true + # activate-environment: dlp # - uses: mamba-org/setup-micromamba@v1 # with: From c5f54edc79220382fb5f3a17664bdbfb8bfbae00 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 15:16:57 -0400 Subject: [PATCH 12/33] fix env --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index e0c9329ef..520e8eba3 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -26,7 +26,7 @@ jobs: id: cached-mamba-env uses: actions/cache@v3 with: - path: ${{ env.CONDA }}/envs + path: /usr/share/miniconda3/envs/dlp key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} restore-keys: mamba-env-${{ runner.os }}- From 8b88ac899fde13e531eaf8649762f01d74932d72 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 15:22:06 -0400 Subject: [PATCH 13/33] path fix --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 520e8eba3..bdbc97dfa 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -119,7 +119,7 @@ jobs: id: cached-mamba-env uses: actions/cache@v3 with: - path: ${{ env.CONDA }}/envs + path: /usr/share/miniconda3/envs/dlp key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} restore-keys: mamba-env-${{ runner.os }}- From d572d687f49ad06bc46898bc1f156f8148662a6b Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:22:30 -0400 Subject: [PATCH 14/33] cache fix --- .github/workflows/backend.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index bdbc97dfa..4b39a5fda 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -40,6 +40,7 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp + use-only-tar-bz2: true # - uses: mamba-org/setup-micromamba@v1 # with: @@ -133,6 +134,7 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp + use-only-tar-bz2: true # - uses: conda-incubator/setup-miniconda@v2 # with: From 62718f359631fa753ce1dfbbc4175cf06b60cb3d Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:26:50 -0400 Subject: [PATCH 15/33] CACHE_NUMBER to reset cache --- .github/workflows/backend.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 4b39a5fda..3f1e7f26a 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -119,10 +119,13 @@ jobs: - name: Load Cached Mamba Env id: cached-mamba-env uses: actions/cache@v3 + env: + # Increase this value to reset cache if etc/example-environment.yml has not changed + CACHE_NUMBER: 0 with: path: /usr/share/miniconda3/envs/dlp key: - mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} + mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} restore-keys: mamba-env-${{ runner.os }}- From 7ea84e84ce7f2f8e295e6be345dc766c3e5267f3 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:28:36 -0400 Subject: [PATCH 16/33] restore keys keys hint removed --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 3f1e7f26a..9b489febb 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -126,7 +126,7 @@ jobs: path: /usr/share/miniconda3/envs/dlp key: mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} - restore-keys: mamba-env-${{ runner.os }}- + #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env From c8cc0f9359b4b7493490eb9901f8a1e1ad473461 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:32:16 -0400 Subject: [PATCH 17/33] cache number --- .github/workflows/backend.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 9b489febb..9c4579401 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -25,11 +25,14 @@ jobs: - name: Load Cached Mamba Env id: cached-mamba-env uses: actions/cache@v3 + env: + # Increase this value to reset cache if etc/example-environment.yml has not changed + CACHE_NUMBER: 0 with: path: /usr/share/miniconda3/envs/dlp key: - mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} - restore-keys: mamba-env-${{ runner.os }}- + mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} + #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env From 5ddc93385ed480206c7f6f5ec74519de96306845 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:34:48 -0400 Subject: [PATCH 18/33] bump cache number --- .github/workflows/backend.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 9c4579401..de920f1dd 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -27,7 +27,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 0 + CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp key: @@ -124,7 +124,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 0 + CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp key: From 0d00db8ca082c52664f1d8dca67bde6a5459965f Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:43:54 -0400 Subject: [PATCH 19/33] poetry run append --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index de920f1dd..b1636189b 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -193,7 +193,7 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 - cd training && pytest tests + cd training && poetry run pytest tests shell: bash -el {0} #shell: micromamba-shell {0} From fb8a8d8511151ba8e691fd2e01953021680e9ba0 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:51:15 -0400 Subject: [PATCH 20/33] no cleanup --- .github/workflows/backend.yml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index b1636189b..7d7634fb5 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -27,7 +27,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 1 + CACHE_NUMBER: 2 with: path: /usr/share/miniconda3/envs/dlp key: @@ -43,7 +43,8 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - use-only-tar-bz2: true + run-post: false + #use-only-tar-bz2: true # - uses: mamba-org/setup-micromamba@v1 # with: @@ -124,7 +125,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 1 + CACHE_NUMBER: 2 with: path: /usr/share/miniconda3/envs/dlp key: @@ -140,7 +141,8 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - use-only-tar-bz2: true + run-post: false + #use-only-tar-bz2: true # - uses: conda-incubator/setup-miniconda@v2 # with: @@ -193,6 +195,8 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 + conda envs --list + pwd cd training && poetry run pytest tests shell: bash -el {0} #shell: micromamba-shell {0} From 0c2538b339d214388b45d70310ffe884731c5f61 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 16:57:15 -0400 Subject: [PATCH 21/33] typo --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 7d7634fb5..4163e514d 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -195,7 +195,7 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 - conda envs --list + conda env --list pwd cd training && poetry run pytest tests shell: bash -el {0} From a93915af45319514e38e2d561c16198c86c2099b Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 17:00:38 -0400 Subject: [PATCH 22/33] remove --list in conda env command --- .github/workflows/backend.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 4163e514d..7b84167dc 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -195,7 +195,7 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 - conda env --list + conda env list pwd cd training && poetry run pytest tests shell: bash -el {0} From d65d66ca21fdfbaf6fe85a83b37e81fc817823a9 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 17:11:50 -0400 Subject: [PATCH 23/33] adjust shell name --- .github/workflows/backend.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 7b84167dc..79d815204 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -142,7 +142,6 @@ jobs: use-mamba: true activate-environment: dlp run-post: false - #use-only-tar-bz2: true # - uses: conda-incubator/setup-miniconda@v2 # with: @@ -198,6 +197,6 @@ jobs: conda env list pwd cd training && poetry run pytest tests - shell: bash -el {0} + shell: bash -l {0} #shell: micromamba-shell {0} From 8ac002ea67cf6062f6e8b3e0e82d097ecfd69263 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 17:40:18 -0400 Subject: [PATCH 24/33] poetry cache number --- .github/workflows/backend.yml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 79d815204..47422668b 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -61,10 +61,13 @@ jobs: - name: Load cached venv id: cached-poetry-dependencies uses: actions/cache@v3 + env: + # Increase this value to reset cache if poetry.lock has not changed + CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp - key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} - restore-keys: training-venv-${{ runner.os }}- + key: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/poetry.lock') }} + restore-keys: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}- # - name: Load cached venv # id: cached-poetry-dependencies # uses: actions/cache@v3 @@ -166,10 +169,13 @@ jobs: - name: Load cached venv id: cached-poetry-dependencies uses: actions/cache@v3 + env: + # Increase this value to reset cache if poetry.lock has not changed + CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp - key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} - restore-keys: training-venv-${{ runner.os }}- + key: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/poetry.lock') }} + restore-keys: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}- # - name: Load cached venv # id: cached-poetry-dependencies From 33ada0c689e43af9e64d30e77096c7b519b55f72 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 17:43:29 -0400 Subject: [PATCH 25/33] bump cache number --- .github/workflows/backend.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 47422668b..8e4d34510 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -27,7 +27,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 2 + CACHE_NUMBER: 3 with: path: /usr/share/miniconda3/envs/dlp key: @@ -43,7 +43,7 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - run-post: false + # run-post: false #use-only-tar-bz2: true # - uses: mamba-org/setup-micromamba@v1 @@ -128,7 +128,7 @@ jobs: uses: actions/cache@v3 env: # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 2 + CACHE_NUMBER: 3 with: path: /usr/share/miniconda3/envs/dlp key: @@ -144,7 +144,7 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - run-post: false + #run-post: false # - uses: conda-incubator/setup-miniconda@v2 # with: From 3f04e2b2978101a3ba167ada624f6296060e255d Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 17:50:56 -0400 Subject: [PATCH 26/33] backend.yml fix --- .github/workflows/backend.yml | 62 +++++++++++++++-------------------- 1 file changed, 27 insertions(+), 35 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 8e4d34510..c78cd4024 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -22,17 +22,17 @@ jobs: # - name: Setup tmate session # uses: mxschmitt/action-tmate@v3 - - name: Load Cached Mamba Env - id: cached-mamba-env - uses: actions/cache@v3 - env: - # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 3 - with: - path: /usr/share/miniconda3/envs/dlp - key: - mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} - #restore-keys: mamba-env-${{ runner.os }}- + # - name: Load Cached Mamba Env + # id: cached-mamba-env + # uses: actions/cache@v3 + # env: + # # Increase this value to reset cache if etc/example-environment.yml has not changed + # CACHE_NUMBER: 3 + # with: + # path: /usr/share/miniconda3/envs/dlp + # key: + # mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} + # #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env @@ -43,8 +43,6 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - # run-post: false - #use-only-tar-bz2: true # - uses: mamba-org/setup-micromamba@v1 # with: @@ -61,13 +59,10 @@ jobs: - name: Load cached venv id: cached-poetry-dependencies uses: actions/cache@v3 - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp - key: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/poetry.lock') }} - restore-keys: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}- + key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} + restore-keys: training-venv-${{ runner.os }}- # - name: Load cached venv # id: cached-poetry-dependencies # uses: actions/cache@v3 @@ -123,17 +118,17 @@ jobs: - name: Check out repository uses: actions/checkout@v3 - - name: Load Cached Mamba Env - id: cached-mamba-env - uses: actions/cache@v3 - env: - # Increase this value to reset cache if etc/example-environment.yml has not changed - CACHE_NUMBER: 3 - with: - path: /usr/share/miniconda3/envs/dlp - key: - mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} - #restore-keys: mamba-env-${{ runner.os }}- + # - name: Load Cached Mamba Env + # id: cached-mamba-env + # uses: actions/cache@v3 + # env: + # # Increase this value to reset cache if etc/example-environment.yml has not changed + # CACHE_NUMBER: 3 + # with: + # path: /usr/share/miniconda3/envs/dlp + # key: + # mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} + # #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env @@ -169,13 +164,10 @@ jobs: - name: Load cached venv id: cached-poetry-dependencies uses: actions/cache@v3 - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 with: path: /usr/share/miniconda3/envs/dlp - key: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/poetry.lock') }} - restore-keys: training-venv-${{ runner.os }}-${{ env.CACHE_NUMBER }}- + key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} + restore-keys: training-venv-${{ runner.os }}- # - name: Load cached venv # id: cached-poetry-dependencies @@ -203,6 +195,6 @@ jobs: conda env list pwd cd training && poetry run pytest tests - shell: bash -l {0} + shell: bash -el {0} #shell: micromamba-shell {0} From 9207ac41c325008480bbdbbafec71931237f7b5f Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 18:02:03 -0400 Subject: [PATCH 27/33] clean up commented out code in backend.yml --- .github/workflows/backend.yml | 71 ----------------------------------- 1 file changed, 71 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index c78cd4024..d9bc9120c 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -19,20 +19,6 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 - # - name: Setup tmate session - # uses: mxschmitt/action-tmate@v3 - - # - name: Load Cached Mamba Env - # id: cached-mamba-env - # uses: actions/cache@v3 - # env: - # # Increase this value to reset cache if etc/example-environment.yml has not changed - # CACHE_NUMBER: 3 - # with: - # path: /usr/share/miniconda3/envs/dlp - # key: - # mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} - # #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env @@ -43,15 +29,6 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - - # - uses: mamba-org/setup-micromamba@v1 - # with: - # micromamba-version: '1.4.5-0' - # environment-file: training/environment.yml - # init-shell: >- - # bash - # cache-environment: true - # cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} #---------------------------------------------- # load cached venv if cache exists @@ -63,13 +40,6 @@ jobs: path: /usr/share/miniconda3/envs/dlp key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} restore-keys: training-venv-${{ runner.os }}- - # - name: Load cached venv - # id: cached-poetry-dependencies - # uses: actions/cache@v3 - # with: - # path: /home/runner/micromamba/envs/dlp/ - # key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} - # restore-keys: training-venv-${{ runner.os }}- #--------------------------------------------------- # install dependencies if cache does not exist @@ -79,7 +49,6 @@ jobs: if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: pwd && cd training && poetry install --no-interaction --no-root && poetry env info -p shell: bash -el {0} - #shell: micromamba-shell {0} #---------------------------------------------- # pyright static checker @@ -117,18 +86,6 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 - - # - name: Load Cached Mamba Env - # id: cached-mamba-env - # uses: actions/cache@v3 - # env: - # # Increase this value to reset cache if etc/example-environment.yml has not changed - # CACHE_NUMBER: 3 - # with: - # path: /usr/share/miniconda3/envs/dlp - # key: - # mamba-env-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/training/environment.yml') }} - # #restore-keys: mamba-env-${{ runner.os }}- - name: Install Mamba Env @@ -139,23 +96,6 @@ jobs: miniforge-version: latest use-mamba: true activate-environment: dlp - #run-post: false - - # - uses: conda-incubator/setup-miniconda@v2 - # with: - # environment-file: training/environment.yml - # miniforge-version: latest - # use-mamba: true - # activate-environment: dlp - - # - uses: mamba-org/setup-micromamba@v1 - # with: - # micromamba-version: '1.4.5-0' - # environment-file: training/environment.yml - # init-shell: >- - # bash - # cache-environment: true - # cache-environment-key: mamba-env-${{ runner.os }}-${{ hashFiles('**/training/environment.yml') }} #---------------------------------------------- # load cached venv if cache exists @@ -169,13 +109,6 @@ jobs: key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} restore-keys: training-venv-${{ runner.os }}- - # - name: Load cached venv - # id: cached-poetry-dependencies - # uses: actions/cache@v3 - # with: - # path: /home/runner/micromamba/envs/dlp/ - # key: training-venv-${{ runner.os }}-${{ hashFiles('**/training/poetry.lock') }} - # restore-keys: training-venv-${{ runner.os }}- #---------------------------------------------- # install dependencies if cache does not exist #---------------------------------------------- @@ -183,7 +116,6 @@ jobs: if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: cd training && poetry install --no-interaction --no-root shell: bash -el {0} - #shell: micromamba-shell {0} #---------------------------------------------- # run test suite #---------------------------------------------- @@ -192,9 +124,6 @@ jobs: export AWS_ACCESS_KEY_ID=testing export AWS_SECRET_ACCESS_KEY=testing export AWS_DEFAULT_REGION=us-west-2 - conda env list - pwd cd training && poetry run pytest tests shell: bash -el {0} - #shell: micromamba-shell {0} From b6b7ef2bf23c3dd6b08286f7423d6ed98a15e49f Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 18:03:47 -0400 Subject: [PATCH 28/33] remove unused code --- .github/workflows/backend.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index d9bc9120c..3a56ccd0c 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -22,7 +22,6 @@ jobs: - name: Install Mamba Env - if: steps.cached-mamba-env.outputs.cache-hit != 'true' uses: conda-incubator/setup-miniconda@v2 with: environment-file: training/environment.yml @@ -89,7 +88,6 @@ jobs: - name: Install Mamba Env - if: steps.cached-mamba-env.outputs.cache-hit != 'true' uses: conda-incubator/setup-miniconda@v2 with: environment-file: training/environment.yml From 1c12b7cd2ef7a1933b5660919f60567545c6fb62 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sat, 7 Oct 2023 18:36:26 -0400 Subject: [PATCH 29/33] cache implemented --- .github/workflows/backend.yml | 44 +++++++++++++++++++++++++++++------ 1 file changed, 37 insertions(+), 7 deletions(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 3a56ccd0c..724270e32 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -19,16 +19,31 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 - - - name: Install Mamba Env + - name: Setup Mamba uses: conda-incubator/setup-miniconda@v2 with: - environment-file: training/environment.yml miniforge-version: latest use-mamba: true activate-environment: dlp + - name: Cache Mamba env + id: cached-mamba-env + uses: actions/cache@v3 + env: + # Increase this value to reset cache if etc/example-environment.yml has not changed + CACHE_NUMBER: 0 + with: + path: /usr/share/miniconda3/envs/ + key: + mamba-${{ runner.os }}-${{env.CACHE_NUMBER }}-${{hashFiles('**/training/environment.yml') }} + + - name: Update environment + run: + mamba env update -n dlp -f + training/environment.yml + if: steps.cached-mamba-env.outputs.cache-hit != 'true' + #---------------------------------------------- # load cached venv if cache exists #---------------------------------------------- @@ -85,16 +100,31 @@ jobs: #---------------------------------------------- - name: Check out repository uses: actions/checkout@v3 - - - - name: Install Mamba Env + + - name: Setup Mamba uses: conda-incubator/setup-miniconda@v2 with: - environment-file: training/environment.yml miniforge-version: latest use-mamba: true activate-environment: dlp + - name: Cache Mamba env + id: cached-mamba-env + uses: actions/cache@v3 + env: + # Increase this value to reset cache if etc/example-environment.yml has not changed + CACHE_NUMBER: 0 + with: + path: /usr/share/miniconda3/envs/ + key: + mamba-${{ runner.os }}-${{env.CACHE_NUMBER }}-${{hashFiles('**/training/environment.yml') }} + + - name: Update environment + run: + mamba env update -n dlp -f + training/environment.yml + if: steps.cached-mamba-env.outputs.cache-hit != 'true' + #---------------------------------------------- # load cached venv if cache exists #---------------------------------------------- From 4a10a1a82936af082e9a5e4ea86798f9b4451714 Mon Sep 17 00:00:00 2001 From: karkir0003 Date: Sun, 8 Oct 2023 15:26:29 -0400 Subject: [PATCH 30/33] poetry to path + remove legacy lib arg --- .github/workflows/backend.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/backend.yml b/.github/workflows/backend.yml index 724270e32..24adeebaa 100644 --- a/.github/workflows/backend.yml +++ b/.github/workflows/backend.yml @@ -64,6 +64,9 @@ jobs: run: pwd && cd training && poetry install --no-interaction --no-root && poetry env info -p shell: bash -el {0} + - name: Add Poetry env to PATH + run: cd training && echo "$(poetry env info --path)/bin" >> $GITHUB_PATH + shell: bash -el {0} #---------------------------------------------- # pyright static checker #---------------------------------------------- @@ -73,7 +76,6 @@ jobs: with: github_token: ${{ secrets.GITHUB_TOKEN }} # You need this reporter: github-pr-review # Change reporter. - lib: true #---------------------------------------------- # black formatter @@ -144,6 +146,10 @@ jobs: if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: cd training && poetry install --no-interaction --no-root shell: bash -el {0} + + - name: Add Poetry env to PATH + run: cd training && echo "$(poetry env info --path)/bin" >> $GITHUB_PATH + shell: bash -el {0} #---------------------------------------------- # run test suite #---------------------------------------------- From 53af8a468d75fcf67201293f81babe5f3380c104 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Fri, 13 Oct 2023 22:15:00 -0400 Subject: [PATCH 31/33] new changes --- training/tests/test_loss_function.py | 1 - training/tests/test_model.py | 12 ------------ training/training/core/dl_model.py | 1 - 3 files changed, 14 deletions(-) diff --git a/training/tests/test_loss_function.py b/training/tests/test_loss_function.py index bee1ddc6c..8f2303bff 100644 --- a/training/tests/test_loss_function.py +++ b/training/tests/test_loss_function.py @@ -49,7 +49,6 @@ def test_mse_loss_computation_correct(output, labels, expected_number): loss_function_name = "MSELOSS" loss_function = getCriterionHandler("MSELOSS") computed_loss = compute_loss(loss_function_name, output, labels) - print(torch.sqrt(computed_loss)) assert pytest.approx(expected_number) == torch.sqrt(computed_loss) diff --git a/training/tests/test_model.py b/training/tests/test_model.py index c1a4a098d..7883a4d35 100644 --- a/training/tests/test_model.py +++ b/training/tests/test_model.py @@ -13,19 +13,7 @@ ], ) def test_dlmodel(input_list): - print("input_list: " + str(input_list) + " is of type " + str(type(input_list))) my_model = DLModel(input_list) - print("my_model: " + str(my_model) + " is of type " + str(type(my_model))) - print( - "[module for module in my_model.model.modules() if not isinstance(module, nn.Sequential)]: " - + str( - [ - module - for module in my_model.model.modules() - if not isinstance(module, nn.Sequential) - ] - ) - ) assert [ module for module in my_model.model.modules() diff --git a/training/training/core/dl_model.py b/training/training/core/dl_model.py index 63c45ad87..052ea2199 100644 --- a/training/training/core/dl_model.py +++ b/training/training/core/dl_model.py @@ -39,7 +39,6 @@ def fromLayerParamsList(cls, layer_params_list: list[LayerParams]): return cls(layer_list) def build_model(self, layer_list): - print("Hello World") model = nn.Sequential() ctr = 1 for layer in layer_list: From a9e9e4fd8530fd17e7022455fdaa17de091f0166 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Fri, 13 Oct 2023 22:16:53 -0400 Subject: [PATCH 32/33] code cleanup commit --- backend/tests/test_model.py | 13 ------------- backend/tests/test_model_parser.py | 6 ------ 2 files changed, 19 deletions(-) diff --git a/backend/tests/test_model.py b/backend/tests/test_model.py index aa89fbce6..685708215 100644 --- a/backend/tests/test_model.py +++ b/backend/tests/test_model.py @@ -1,6 +1,5 @@ import pytest import torch.nn as nn -from torch.autograd import Variable from dl.dl_model import * @@ -13,19 +12,7 @@ ], ) def test_dlmodel(input_list): - print("input_list: " + str(input_list) + " is of type " + str(type(input_list))) my_model = DLModel(input_list) - print("my_model: " + str(my_model) + " is of type " + str(type(my_model))) - print( - "[module for module in my_model.model.modules() if not isinstance(module, nn.Sequential)]: " - + str( - [ - module - for module in my_model.model.modules() - if not isinstance(module, nn.Sequential) - ] - ) - ) assert [ module for module in my_model.model.modules() diff --git a/backend/tests/test_model_parser.py b/backend/tests/test_model_parser.py index 9628cf947..927875e3a 100644 --- a/backend/tests/test_model_parser.py +++ b/backend/tests/test_model_parser.py @@ -1,6 +1,5 @@ import pytest import torch.nn as nn -from torch.autograd import Variable from dl.dl_model_parser import * # come up with the expected parsing @@ -27,9 +26,4 @@ ], ) def test_parse_user_architecture(user_model, expected): - print( - "parse_user_architecture(user_model): " - + str(parse_deep_user_architecture(user_model)) - ) - print("expected: " + str(expected)) assert [i == j for i, j in zip(parse_deep_user_architecture(user_model), expected)] From f2569114dd4785a07d7634aacd82fec6caf4ce14 Mon Sep 17 00:00:00 2001 From: Prisha Vallamsetti Date: Fri, 13 Oct 2023 22:21:15 -0400 Subject: [PATCH 33/33] removed line --- training/tests/test_loss_function.py | 1 - 1 file changed, 1 deletion(-) diff --git a/training/tests/test_loss_function.py b/training/tests/test_loss_function.py index 8f2303bff..98f06e975 100644 --- a/training/tests/test_loss_function.py +++ b/training/tests/test_loss_function.py @@ -47,7 +47,6 @@ def test_l1_loss_computation_correct(output, labels, expected_number): ) def test_mse_loss_computation_correct(output, labels, expected_number): loss_function_name = "MSELOSS" - loss_function = getCriterionHandler("MSELOSS") computed_loss = compute_loss(loss_function_name, output, labels) assert pytest.approx(expected_number) == torch.sqrt(computed_loss)