From 143a6484666fe35cc42e1c97f47743aa00b21cfb Mon Sep 17 00:00:00 2001 From: Tara Nitka Date: Tue, 23 Apr 2024 14:17:22 -0700 Subject: [PATCH 1/6] pin numpy to 1.22.3 when using the Blazing Signature Filter and on Windows --- environment_BSF.yml | 2 +- environment_Windows.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment_BSF.yml b/environment_BSF.yml index 7b58505..c1a56e1 100644 --- a/environment_BSF.yml +++ b/environment_BSF.yml @@ -10,7 +10,7 @@ dependencies: - pyarrow - jinja2 - matplotlib - - numpy >= 1.22.3 + - numpy == 1.22.3 - numba >= 0.56 - scipy - pandas diff --git a/environment_Windows.yml b/environment_Windows.yml index e769414..38e14ea 100644 --- a/environment_Windows.yml +++ b/environment_Windows.yml @@ -10,7 +10,7 @@ dependencies: - pyarrow - jinja2 - matplotlib - - numpy >= 1.22.3 + - numpy == 1.22.3 - numba >= 0.56 - scipy - pandas From 742d5cb4f3f45cd62f4f3f6987aac4eb2564375f Mon Sep 17 00:00:00 2001 From: christinehc Date: Wed, 8 May 2024 14:01:05 -0700 Subject: [PATCH 2/6] fix: pin hdbscan version. install snekmer directly from pip changelog: - Require hdbscan >= 0.8.29 to resolve installation errors (see: https://github.com/scikit-learn-contrib/hdbscan/issues/565) - Directly use available pip installable version of snekmer instead of git+github functionality --- environment.yml | 4 ++-- environment_BSF.yml | 4 ++-- environment_Windows.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 5d5da73..03001c8 100644 --- a/environment.yml +++ b/environment.yml @@ -19,7 +19,7 @@ dependencies: - snakemake == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan + - hdbscan >= 0.8.29 - pip - pip: - - -e git+https://github.com/PNNL-CompBio/Snekmer#egg=snekmer + - snekmer diff --git a/environment_BSF.yml b/environment_BSF.yml index c1a56e1..0d6ccd4 100644 --- a/environment_BSF.yml +++ b/environment_BSF.yml @@ -19,8 +19,8 @@ dependencies: - snakemake == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan + - hdbscan >= 0.8.29 - pip - pip: - - -e git+https://github.com/PNNL-CompBio/Snekmer#egg=snekmer + - snekmer - -e git+https://github.com/PNNL-Compbio/bsf-jaccard-py#egg=bsf diff --git a/environment_Windows.yml b/environment_Windows.yml index 38e14ea..0a1fa85 100644 --- a/environment_Windows.yml +++ b/environment_Windows.yml @@ -19,7 +19,7 @@ dependencies: - snakemake-minimal == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan + - hdbscan >= 0.8.29 - pip - pip: - - -e git+https://github.com/PNNL-CompBio/Snekmer#egg=snekmer + - snekmer From 57539881f2b442553c08d5a766d29bf8f7c27c68 Mon Sep 17 00:00:00 2001 From: Tara Nitka Date: Wed, 5 Jun 2024 14:11:27 -0700 Subject: [PATCH 3/6] add defaults::pyarrow to environment spec, ensuring pyarrow is installed correctly --- environment.yml | 4 ++-- environment_BSF.yml | 2 +- environment_Windows.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 03001c8..880f335 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: snekmer +name: snekmer-test channels: - anaconda - bioconda @@ -7,7 +7,7 @@ channels: dependencies: - python >= 3.9 - biopython - - pyarrow + - defaults::pyarrow - jinja2 - matplotlib - numpy == 1.22.3 diff --git a/environment_BSF.yml b/environment_BSF.yml index 0d6ccd4..d3355e1 100644 --- a/environment_BSF.yml +++ b/environment_BSF.yml @@ -7,7 +7,7 @@ channels: dependencies: - python >= 3.9 - biopython - - pyarrow + - defaults::pyarrow - jinja2 - matplotlib - numpy == 1.22.3 diff --git a/environment_Windows.yml b/environment_Windows.yml index 0a1fa85..4b2b85b 100644 --- a/environment_Windows.yml +++ b/environment_Windows.yml @@ -7,7 +7,7 @@ channels: dependencies: - python >= 3.9 - biopython - - pyarrow + - defaults::pyarrow - jinja2 - matplotlib - numpy == 1.22.3 From 9a5992ad106d42b94a7af66d74dff7d46aed0d83 Mon Sep 17 00:00:00 2001 From: Tara Nitka Date: Wed, 5 Jun 2024 14:46:57 -0700 Subject: [PATCH 4/6] pin hdbscan to 0.8.29 and scikit-learn to 1.2.2 --- environment.yml | 6 +++--- environment_BSF.yml | 4 ++-- environment_Windows.yml | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/environment.yml b/environment.yml index 880f335..e8c8a14 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: snekmer-test +name: snekmer channels: - anaconda - bioconda @@ -15,11 +15,11 @@ dependencies: - scipy - pandas == 1.4.2 - seaborn - - scikit-learn + - scikit-learn == 1.2.2 - snakemake == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan >= 0.8.29 + - hdbscan == 0.8.29 - pip - pip: - snekmer diff --git a/environment_BSF.yml b/environment_BSF.yml index d3355e1..7d80712 100644 --- a/environment_BSF.yml +++ b/environment_BSF.yml @@ -15,11 +15,11 @@ dependencies: - scipy - pandas - seaborn - - scikit-learn + - scikit-learn == 1.2.2 - snakemake == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan >= 0.8.29 + - hdbscan == 0.8.29 - pip - pip: - snekmer diff --git a/environment_Windows.yml b/environment_Windows.yml index 4b2b85b..3ec353c 100644 --- a/environment_Windows.yml +++ b/environment_Windows.yml @@ -15,11 +15,11 @@ dependencies: - scipy - pandas - seaborn - - scikit-learn + - scikit-learn == 1.2.2 - snakemake-minimal == 7.0 - tabulate == 0.8.10 - umap-learn - - hdbscan >= 0.8.29 + - hdbscan == 0.8.29 - pip - pip: - snekmer From 42b0d7d3ffcc5f2ef02fe82bad4fd2a65dc9e572 Mon Sep 17 00:00:00 2001 From: Tara Nitka Date: Tue, 14 Jan 2025 10:19:19 -0800 Subject: [PATCH 5/6] fix glutamic acid being omitted from hydrocharge alphabet --- snekmer/alphabet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snekmer/alphabet.py b/snekmer/alphabet.py index c841edd..32d0507 100644 --- a/snekmer/alphabet.py +++ b/snekmer/alphabet.py @@ -52,7 +52,7 @@ "hydrocharge": { "SFTNYQCWPH": "L", # hydrophilic (L-ove) "VMLAIG": "H", # hydrophobic (H-ate) - "KNDR": "C", # charged (C-harged) + "KNDER": "C", # charged (C-harged) "_keys": "LHC", }, # 2-value hydrophobicity with structural-breakers as a third category From 0fe52d9c7f23426f9efcc28fb317c261fbfed05c Mon Sep 17 00:00:00 2001 From: Tara Nitka Date: Tue, 14 Jan 2025 10:35:49 -0800 Subject: [PATCH 6/6] fix asparagine mapping to two categories in hydrocharge alphabet --- snekmer/alphabet.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/snekmer/alphabet.py b/snekmer/alphabet.py index 32d0507..b9da99d 100644 --- a/snekmer/alphabet.py +++ b/snekmer/alphabet.py @@ -6,6 +6,7 @@ author(s): @biodataganache, @wichne """ + # imports from typing import Dict, Mapping, Set, Union @@ -50,7 +51,7 @@ # 2-value hydrophobicity with charged residues as a third # category. Made by @biodataganache. "hydrocharge": { - "SFTNYQCWPH": "L", # hydrophilic (L-ove) + "SFTYQCWPH": "L", # hydrophilic (L-ove) "VMLAIG": "H", # hydrophobic (H-ate) "KNDER": "C", # charged (C-harged) "_keys": "LHC",