From e8d7258b0dc5694f806d63dbbe3bcc83fb6f6222 Mon Sep 17 00:00:00 2001 From: kierandidi Date: Mon, 8 Apr 2024 15:31:20 +0100 Subject: [PATCH 1/3] [fix] notebook descriptions --- notebooks/adding_new_dataset_tutorial.ipynb | 4 ++-- notebooks/customizing_existing_dataset_tutorial.ipynb | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/notebooks/adding_new_dataset_tutorial.ipynb b/notebooks/adding_new_dataset_tutorial.ipynb index 24bfcb9b..8d84f207 100644 --- a/notebooks/adding_new_dataset_tutorial.ipynb +++ b/notebooks/adding_new_dataset_tutorial.ipynb @@ -352,7 +352,7 @@ "cfg = config.validate_config(cfg)\n", "\n", "datamodule = hydra.utils.instantiate(cfg.dataset.datamodule)\n", - "datamodule.setup(\"train\")\n", + "datamodule.setup(\"fit\")\n", "dl = datamodule.train_dataloader()\n", "\n", "for i in dl:\n", @@ -448,7 +448,7 @@ "cfg = config.validate_config(cfg)\n", "\n", "datamodule = hydra.utils.instantiate(cfg)\n", - "datamodule.setup(\"train\")\n", + "datamodule.setup(\"fit\")\n", "dl = datamodule.train_dataloader()\n", "\n", "for i in dl:\n", diff --git a/notebooks/customizing_existing_dataset_tutorial.ipynb b/notebooks/customizing_existing_dataset_tutorial.ipynb index 165ae867..ea32dc9c 100644 --- a/notebooks/customizing_existing_dataset_tutorial.ipynb +++ b/notebooks/customizing_existing_dataset_tutorial.ipynb @@ -84,7 +84,7 @@ " overrides=[\n", " \"encoder=schnet\",\n", " \"task=inverse_folding\",\n", - " \"dataset=cath\",\n", + " \"dataset=pdb\",\n", " \"features=ca_angles\",\n", " \"+aux_task=none\",\n", " ],\n", @@ -118,7 +118,7 @@ "cfg = config.validate_config(cfg)\n", "\n", "datamodule = hydra.utils.instantiate(cfg.dataset.datamodule)\n", - "datamodule.setup(\"train\")\n", + "datamodule.setup(\"fit\")\n", "dl = datamodule.train_dataloader()\n", "\n", "for i in dl:\n", @@ -207,7 +207,7 @@ "cfg = config.validate_config(cfg)\n", "\n", "datamodule = hydra.utils.instantiate(cfg)\n", - "datamodule.setup(\"train\")\n", + "datamodule.setup(\"fit\")\n", "dl = datamodule.train_dataloader()\n", "\n", "for i in dl:\n", From 16f651349d2fe10ff1d5ef8f8907d62bf6f3be50 Mon Sep 17 00:00:00 2001 From: kierandidi Date: Mon, 8 Apr 2024 18:17:25 +0100 Subject: [PATCH 2/3] Added to changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95afd0f0..21694246 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ ### 0.2.6 (UNRELEASED) ### Datasets +* Correct stage-based conditions mentioned in notebook tutorials [#92](https://github.com/a-r-j/ProteinWorkshop/pull/92) * Add stage-based conditions to `setup` in `ProteinDataModule` [#72](https://github.com/a-r-j/ProteinWorkshop/pull/72) * Improves support for datamodules with multiple test sets. Generalises this to support GO and FOLD. Also adds multiple seq ID.-based splits for GO. [#72](https://github.com/a-r-j/ProteinWorkshop/pull/72) * Add redownload checks for already downloaded datasets and harmonise pdb download interface [#86](https://github.com/a-r-j/ProteinWorkshop/pull/86) From b65f3b56f5cea23be97f6a7ec4945c95a3394043 Mon Sep 17 00:00:00 2001 From: kierandidi Date: Tue, 9 Apr 2024 09:50:35 +0100 Subject: [PATCH 3/3] change pdb to cath --- notebooks/customizing_existing_dataset_tutorial.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/customizing_existing_dataset_tutorial.ipynb b/notebooks/customizing_existing_dataset_tutorial.ipynb index ea32dc9c..c8dc43d3 100644 --- a/notebooks/customizing_existing_dataset_tutorial.ipynb +++ b/notebooks/customizing_existing_dataset_tutorial.ipynb @@ -84,7 +84,7 @@ " overrides=[\n", " \"encoder=schnet\",\n", " \"task=inverse_folding\",\n", - " \"dataset=pdb\",\n", + " \"dataset=cath\",\n", " \"features=ca_angles\",\n", " \"+aux_task=none\",\n", " ],\n",