From 2b50473c6ea2158dea431833d6baa5db0f4962e9 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 00:08:49 +1100 Subject: [PATCH 1/7] split cell --- .../train-gnn-to-electric-field.ipynb | 23 ++++++++++++------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb b/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb index 0defa7f..ea5f3f4 100644 --- a/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb +++ b/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb @@ -569,6 +569,20 @@ "from pytorch_lightning.callbacks import TQDMProgressBar" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "c8cb0a08-eea6-41e4-9fd6-158204e26e79", + "metadata": {}, + "outputs": [], + "source": [ + "trainer = pl.Trainer(\n", + " max_epochs=100,\n", + " callbacks=[TQDMProgressBar()], # add progress bar\n", + " accelerator=\"cpu\"\n", + ")" + ] + }, { "cell_type": "code", "execution_count": 14, @@ -2058,13 +2072,6 @@ } ], "source": [ - "trainer = pl.Trainer(\n", - " max_epochs=100,\n", - " callbacks=[TQDMProgressBar()], # add progress bar\n", - " accelerator=\"cpu\"\n", - ")\n", - "\n", - "\n", "trainer.fit(\n", " training_model,\n", " datamodule=training_model.create_data_module(verbose=False),\n", @@ -2137,7 +2144,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.5" + "version": "3.11.4" } }, "nbformat": 4, From df04a0841583913f85df531020f495a508ddaa2d Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 00:27:42 +1100 Subject: [PATCH 2/7] split cell further --- .../train-gnn-to-electric-field.ipynb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb b/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb index ea5f3f4..2e918cd 100644 --- a/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb +++ b/examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb @@ -583,6 +583,16 @@ ")" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "f8846142-77f2-4d60-a74e-c3bc3c3ed3ee", + "metadata": {}, + "outputs": [], + "source": [ + "datamodule = training_model.create_data_module(verbose=False)" + ] + }, { "cell_type": "code", "execution_count": 14, @@ -2074,7 +2084,7 @@ "source": [ "trainer.fit(\n", " training_model,\n", - " datamodule=training_model.create_data_module(verbose=False),\n", + " datamodule=datamodule,\n", ")" ] }, From 3aaf171f358ce63f39f98add7a21de50d73a4537 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 00:46:57 +1100 Subject: [PATCH 3/7] see if extending timeout works --- .github/workflows/examples-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/examples-ci.yaml b/.github/workflows/examples-ci.yaml index bacb651..61b4e0b 100644 --- a/.github/workflows/examples-ci.yaml +++ b/.github/workflows/examples-ci.yaml @@ -89,4 +89,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --dist loadscope examples + python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --dist --nbval-cell-timeout=3000 loadscope examples From c1f245f64679f21e61dd63302ac42b1057995a73 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 00:53:20 +1100 Subject: [PATCH 4/7] oops pasted in the middle of dist --- .github/workflows/examples-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/examples-ci.yaml b/.github/workflows/examples-ci.yaml index 61b4e0b..afe7dc1 100644 --- a/.github/workflows/examples-ci.yaml +++ b/.github/workflows/examples-ci.yaml @@ -89,4 +89,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --dist --nbval-cell-timeout=3000 loadscope examples + python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=3000 --dist loadscope examples From a1e83c7e717f265934ce1fd807b6bcecb89a4bae Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 17:01:30 +1100 Subject: [PATCH 5/7] make timeout much higher --- .github/workflows/examples-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/examples-ci.yaml b/.github/workflows/examples-ci.yaml index afe7dc1..20e7988 100644 --- a/.github/workflows/examples-ci.yaml +++ b/.github/workflows/examples-ci.yaml @@ -89,4 +89,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=3000 --dist loadscope examples + python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=10000 --dist loadscope examples From da623f78ee479f0bb3920a1148046011a0d3aba2 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 20:46:42 +1100 Subject: [PATCH 6/7] even higher --- .github/workflows/examples-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/examples-ci.yaml b/.github/workflows/examples-ci.yaml index 20e7988..0d3dc98 100644 --- a/.github/workflows/examples-ci.yaml +++ b/.github/workflows/examples-ci.yaml @@ -89,4 +89,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=10000 --dist loadscope examples + python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=50000 --dist loadscope examples From 21d23b84282fd694d48149cad70fdd5ace4dd86a Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Mon, 14 Oct 2024 22:37:18 +1100 Subject: [PATCH 7/7] stop mac examples for now --- .github/workflows/examples-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/examples-ci.yaml b/.github/workflows/examples-ci.yaml index 0d3dc98..ddc1035 100644 --- a/.github/workflows/examples-ci.yaml +++ b/.github/workflows/examples-ci.yaml @@ -30,7 +30,7 @@ jobs: strategy: fail-fast: false matrix: - os: [macOS-12, ubuntu-latest] + os: [ubuntu-latest] python-version: ["3.11", "3.12"] pydantic-version: ["2"] include-rdkit: [true]