From fba8c4c29762d746333c8803ac62253b173a272f Mon Sep 17 00:00:00 2001 From: hertelj Date: Thu, 16 May 2024 15:02:15 +0200 Subject: [PATCH 1/7] Fixing package releases and names Using Chemprob 1.5.1 --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 2e76e617..17f96bfe 100644 --- a/setup.py +++ b/setup.py @@ -29,9 +29,9 @@ "keras==2.9.0", "tensorflow-gpu==2.9.3", "wandb~=0.12.0", - "umap~=0.1.1", + "umap-learn~=0.1.1", "seaborn~=0.12.2", - "chemprop @ git+https://github.com/soulios/chemprop.git@1d73523e49aa28a90b74edc04aaf45d7e124e338", + "chemprop~=1.5.1" ], entry_points={"console_scripts": ["dfpl=dfpl.__main__:main"]}, ) From f40d67afaf59ed2d1c17d49136bd8181db993df1 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 11 Jun 2024 11:03:09 +0200 Subject: [PATCH 2/7] make github workflow more verbose --- .github/workflows/pr.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml index 27f43c34..2cde11f5 100644 --- a/.github/workflows/pr.yml +++ b/.github/workflows/pr.yml @@ -62,7 +62,7 @@ jobs: - name: Run test CLI calls for example run: | - set -e + set -ex dfpl train -f example/train.json if [ ! -d example/results_train/ ]; then echo "training result directory missing" >&2 @@ -102,4 +102,4 @@ jobs: fi - dfpl convert -f tests/data \ No newline at end of file + dfpl convert -f tests/data From c1d95457dd8366d9b7441d896d1efb3de16c1b29 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 11 Jun 2024 12:14:53 +0200 Subject: [PATCH 3/7] remove tree --- .github/workflows/pr.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml index 2cde11f5..fb67d09b 100644 --- a/.github/workflows/pr.yml +++ b/.github/workflows/pr.yml @@ -68,7 +68,7 @@ jobs: echo "training result directory missing" >&2 exit 1 fi - tree example + # tree example dfpl predict -f example/predict.json if [ ! -d example/results_predict/ ]; then @@ -80,21 +80,20 @@ jobs: echo "predict result should have at least 6 lines. But had only $(cat example/results_predict/smiles.csv | wc -l)" >&2 exit 1 fi - tree example + # tree example dfpl traingnn -f example/traingnn.json if [ ! -d dmpnn-random/ ]; then echo "predict result directory missing" >&2 exit 1 fi - tree example + # tree example dfpl predictgnn -f example/predictgnn.json if [ ! -d preds_dmpnn/ ]; then echo "predict result directory missing" >&2 exit 1 fi - echo "result lines "$(wc -l preds_dmpnn/DMPNN_preds.csv) if [ "$(cat preds_dmpnn/DMPNN_preds.csv | wc -l)" -lt "6" ]; then echo "predict result should have at least 5 lines. But had only $(cat preds_dmpnn/DMPNN_preds.csv | wc -l)" >&2 From 543cc571831e293cfb220c4d79a0d43286d962e5 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 12 Jun 2024 14:27:29 +0200 Subject: [PATCH 4/7] use latest 1.x chemprop which has the needed extra-metrics (implemented there in https://github.com/chemprop/chemprop/pull/542) --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 17f96bfe..6d9defaf 100644 --- a/setup.py +++ b/setup.py @@ -31,7 +31,7 @@ "wandb~=0.12.0", "umap-learn~=0.1.1", "seaborn~=0.12.2", - "chemprop~=1.5.1" + "chemprop~=1.7.1" ], entry_points={"console_scripts": ["dfpl=dfpl.__main__:main"]}, ) From c5646f6bc32c942fa319266683bf23369ba1ecd0 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 12 Jun 2024 14:49:19 +0200 Subject: [PATCH 5/7] remove specificity still not in chemprop 1.7 --- example/traingnn.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/example/traingnn.json b/example/traingnn.json index 7a5a0712..714fa80a 100644 --- a/example/traingnn.json +++ b/example/traingnn.json @@ -9,6 +9,6 @@ "split_type": "random", "dataset_type": "classification", "smiles_columns": "smiles", - "extra_metrics": ["balanced_accuracy","auc","f1","mcc","recall","specificity","precision"], + "extra_metrics": ["balanced_accuracy","auc","f1","mcc","recall","precision"], "hidden_size": 256 -} \ No newline at end of file +} From 197545eb3db088d21095fefe9d598f1af1e28038 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 12 Jun 2024 14:50:28 +0200 Subject: [PATCH 6/7] add missing comma --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6d9defaf..42c22c0c 100644 --- a/setup.py +++ b/setup.py @@ -31,7 +31,7 @@ "wandb~=0.12.0", "umap-learn~=0.1.1", "seaborn~=0.12.2", - "chemprop~=1.7.1" + "chemprop~=1.7.1", ], entry_points={"console_scripts": ["dfpl=dfpl.__main__:main"]}, ) From 3a0b4d6ee90ab7382251feeab3a01626bfc82c6d Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 12 Jun 2024 17:01:15 +0200 Subject: [PATCH 7/7] re-add tree --- .github/workflows/pr.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml index fb67d09b..56df68fc 100644 --- a/.github/workflows/pr.yml +++ b/.github/workflows/pr.yml @@ -68,7 +68,7 @@ jobs: echo "training result directory missing" >&2 exit 1 fi - # tree example + tree example dfpl predict -f example/predict.json if [ ! -d example/results_predict/ ]; then @@ -80,14 +80,14 @@ jobs: echo "predict result should have at least 6 lines. But had only $(cat example/results_predict/smiles.csv | wc -l)" >&2 exit 1 fi - # tree example + tree example dfpl traingnn -f example/traingnn.json if [ ! -d dmpnn-random/ ]; then echo "predict result directory missing" >&2 exit 1 fi - # tree example + tree example dfpl predictgnn -f example/predictgnn.json if [ ! -d preds_dmpnn/ ]; then @@ -100,5 +100,4 @@ jobs: exit 1 fi - dfpl convert -f tests/data