From ef89c5b7312a766ea58d0c557d096268bc211393 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 12:14:43 -0700 Subject: [PATCH 1/6] test nbval timeout --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 5d36ed1..5fb12a5 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -64,4 +64,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -v --nbval-lax --nbval-cell-timeout=3000 -n auto --dist loadscope + python -m pytest -v --nbval-lax --nbval-cell-timeout=1 -n auto --dist loadscope From 21adc748af7b8a8891120828deaabb5393a84752 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 12:18:44 -0700 Subject: [PATCH 2/6] bump cell timeout --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 5fb12a5..f75e696 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -64,4 +64,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -v --nbval-lax --nbval-cell-timeout=1 -n auto --dist loadscope + python -m pytest -v --nbval-lax --nbval-cell-timeout=10000 -n auto --dist loadscope From 06386a15eb9416c5e2fe8e1070e7e261b7e7b892 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 12:33:32 -0700 Subject: [PATCH 3/6] update gitignore --- .gitignore | 1 + .../simulation_visualization.ipynb | 27 ++++++++++++++++--- 2 files changed, 24 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 6e57a5b..651d7bb 100644 --- a/.gitignore +++ b/.gitignore @@ -266,6 +266,7 @@ showcase/tyk2_edge.png showcase/tyk2_json/ simulation_visualization/openfe_analysis_skipped/ simulation_visualization/septop_structural_results/ +simulation_visualization/output execution/task*.db execution/warehouse* execution/mcl1_result_jsons/ diff --git a/simulation_visualization/simulation_visualization.ipynb b/simulation_visualization/simulation_visualization.ipynb index dd0c69d..4b0fd4d 100644 --- a/simulation_visualization/simulation_visualization.ipynb +++ b/simulation_visualization/simulation_visualization.ipynb @@ -828,7 +828,18 @@ }, { "cell_type": "code", - "execution_count": 32, + "execution_count": 30, + "id": "56d70f17-12ed-4983-b2ce-eb24c65ff264", + "metadata": {}, + "outputs": [], + "source": [ + "out_dir = pathlib.Path(\"output\")\n", + "out_dir.mkdir(exist_ok=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 31, "id": "a276e16f-3266-41ce-bde2-ece0144fe24a", "metadata": {}, "outputs": [ @@ -859,11 +870,19 @@ "# State B: protein + ligand B\n", "state_b = u_septop_1.select_atoms(\"protein\") + lig_B_1\n", "\n", - "state_b.write(\"septop_state_b_topology.pdb\")\n", - "with mda.Writer(\"septop_out_B.xtc\", n_atoms=len(state_b.atoms)) as w:\n", + "state_b.write(out_dir/\"septop_state_b_topology.pdb\")\n", + "with mda.Writer(str(out_dir/\"septop_out_B.xtc\"), n_atoms=len(state_b.atoms)) as w:\n", " for ts in u_septop_1.trajectory:\n", " w.write(state_b)" ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9ad77aaf-5c6b-4123-bf25-5553eb5977d0", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -882,7 +901,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.13" + "version": "3.13.16" } }, "nbformat": 4, From a96a1f05ecd6f90d6dff1b0dd955fcfe73f1d611 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 12:50:05 -0700 Subject: [PATCH 4/6] update out dir --- simulation_visualization/simulation_visualization.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/simulation_visualization/simulation_visualization.ipynb b/simulation_visualization/simulation_visualization.ipynb index 4b0fd4d..3a76ce4 100644 --- a/simulation_visualization/simulation_visualization.ipynb +++ b/simulation_visualization/simulation_visualization.ipynb @@ -854,8 +854,8 @@ ], "source": [ "# Ligand A\n", - "state_a.write(\"septop_state_a_topology.pdb\")\n", - "with mda.Writer(\"septop_out_A.xtc\", n_atoms=len(state_a.atoms)) as w:\n", + "state_a.write(out_dir/\"septop_state_a_topology.pdb\")\n", + "with mda.Writer(out_dir/\"septop_out_A.xtc\", n_atoms=len(state_a.atoms)) as w:\n", " for ts in u_septop_0.trajectory:\n", " w.write(state_a)" ] From 36f7340f948fde20fa93c06739e209466ed795cd Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 12:50:41 -0700 Subject: [PATCH 5/6] reasonable cell timeout --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index f75e696..d881c9d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -64,4 +64,4 @@ jobs: - name: Run example notebooks run: | - python -m pytest -v --nbval-lax --nbval-cell-timeout=10000 -n auto --dist loadscope + python -m pytest -v --nbval-lax --nbval-cell-timeout=6000 -n auto --dist loadscope From 0cc94f3e4f545b12381ef87356466e4f5316fa94 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 15 Oct 2026 14:09:27 -0700 Subject: [PATCH 6/6] mda writer needs a string --- simulation_visualization/simulation_visualization.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/simulation_visualization/simulation_visualization.ipynb b/simulation_visualization/simulation_visualization.ipynb index 3a76ce4..24d26d2 100644 --- a/simulation_visualization/simulation_visualization.ipynb +++ b/simulation_visualization/simulation_visualization.ipynb @@ -839,7 +839,7 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": null, "id": "a276e16f-3266-41ce-bde2-ece0144fe24a", "metadata": {}, "outputs": [ @@ -855,7 +855,7 @@ "source": [ "# Ligand A\n", "state_a.write(out_dir/\"septop_state_a_topology.pdb\")\n", - "with mda.Writer(out_dir/\"septop_out_A.xtc\", n_atoms=len(state_a.atoms)) as w:\n", + "with mda.Writer(str(out_dir/\"septop_out_A.xtc\"), n_atoms=len(state_a.atoms)) as w:\n", " for ts in u_septop_0.trajectory:\n", " w.write(state_a)" ]