Merge branch 'main' into issue-452

.github/workflows/python-cqa.yml

@@ -24,7 +24,7 @@ jobs:
     - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        key: ${{ runner.os }}-pip-test-${{ hashFiles('pyproject.toml') }}
         restore-keys: |
           ${{ runner.os }}-pip-
     - name: Set up Python ${{ matrix.python-version }}
@@ -40,3 +40,10 @@ jobs:
     - name: Test with pytest
       run: |
         python -m pytest
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/action@v3.0.1

.gitignore

@@ -23,4 +23,4 @@ lint
 uta_*.pgd.gz
 .vscode
 *.log
-.idea
+.idea

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
+      - id: mixed-line-ending
+        args: [ --fix=lf ]
+minimum_pre_commit_version: 4.0.1

Makefile

@@ -47,7 +47,8 @@ venv/%:
 #=> develop: install package in develop mode
 .PHONY: develop setup
 develop setup:
-	pip install -e .[dev,extras,notebooks]
+	pip install -e .[dev,extras,notebooks]; \
+	pre-commit install
 
 #=> devready: create venv, install prerequisites, install pkg in develop mode
 .PHONY: devready

README.md

@@ -192,7 +192,7 @@ This section is intended for developers who contribute to VRS-Python.
 
 ### Installing for development
 
-Fork the repo at <https://github.com/ga4gh/vrs-python/>.
+Fork the repo at <https://github.com/ga4gh/vrs-python/> and initialize a development environment.
 
 ```shell
 git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/vrs-python.git
@@ -201,6 +201,13 @@ make devready
 source venv/3.12/bin/activate
 ```
 
+This setup includes [pre-commit hooks](https://pre-commit.com/). If you create a virtual environment manually, be sure to install the hooks yourself; otherwise, commits may fail during [CI/CD checks](https://github.com/ga4gh/vrs-python/actions/workflows/python-cqa.yml):
+
+```shell
+source venv/3.12/bin/activate
+pre-commit install
+```
+
 If you already cloned the repo, but forgot to include `--recurse-submodules` you can run:
 
 ```shell

docs/setup_help/m1_mac_setup.md

@@ -46,4 +46,4 @@ export PKG_CONFIG_PATH="/opt/homebrew/opt/openssl@1.1/lib/pkgconfig:/opt/homebre
 14. Run the make devready command:
     1. `make devready`
 15. Run the make test command:
-    1. `make test`
+    1. `make test`

docs/setup_help/uta_installation.md

@@ -8,15 +8,15 @@
 4. Create roles for the application, give login and CREATEDB permissions:
    1. `CREATE ROLE uta_admin WITH LOGIN CREATEDB;`
    2. `CREATE ROLE anonymous WITH LOGIN CREATEDB;`
-5. List the users using the command 
+5. List the users using the command
    1. `\du`
 6. Create the UTA Database object
    1. `CREATE DATABASE uta;`
 7. Grant privileges to manage the database to uta_admin
    1. `GRANT ALL PRIVILEGES ON DATABASE uta TO uta_admin;`
 8. Exit postgres
    1. `\q`
-9. Download the UTA database and place it in the uta database object that you created before (**This step takes around 5 hours**). 
+9. Download the UTA database and place it in the uta database object that you created before (**This step takes around 5 hours**).
    1. `export UTA_VERSION=uta_20210129.pgd.gz\ncurl -O http://dl.biocommons.org/uta/$UTA_VERSION\ngzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432`
 10. Set your UTA path
     1. `export UTA_DB_URL=postgresql://uta_admin@localhost:5432/uta/uta_20210129`
@@ -30,4 +30,4 @@ gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localh
     1. `REFRESH MATERIALIZED VIEW uta_20210129.exon_set_exons_fp_mv;`
     2. `REFRESH MATERIALIZED VIEW uta_20210129.tx_exon_set_summary_mv;`
     3. `REFRESH MATERIALIZED VIEW uta_20210129.tx_def_summary_mv;`
-    4. `REFRESH MATERIALIZED VIEW uta_20210129.tx_similarity_mv;` #**This step will take 5 or more hours**
+    4. `REFRESH MATERIALIZED VIEW uta_20210129.tx_similarity_mv;` #**This step will take 5 or more hours**

notebooks/getting_started/README.md

@@ -42,8 +42,3 @@ we show how to transform basic variants to VRS, and in some cases, back to the o
 The final notebook of this series,
 [Exploring the CNV Translator](5_Exploring_the_CnvTranslator.ipynb) details transformations
 of various forms of copy number variation to their VRS representations.
-
-
-
-
-

pyproject.toml

@@ -58,6 +58,7 @@ dev = [
     "vcrpy",
     "pyyaml",
     # style
+    "pre-commit>=4.0.1",
     "pylint",
     "yapf",
     # docs

src/ga4gh/vrs/utils/hgvs_tools.py

@@ -33,7 +33,7 @@ def __init__(self,data_proxy: _DataProxy = None):
         self.variant_mapper = hgvs.variantmapper.VariantMapper(self.uta_conn)
         self.data_proxy = data_proxy
 
-    
+
 
     def close(self):
         # TODO These should only be closed if they are owned by this instance
@@ -57,7 +57,7 @@ def parse(self, hgvs_str):
         if not self.hgvs_re.match(hgvs_str):
             return None
         return self.parser.parse_hgvs_variant(hgvs_str)
-    
+
     def is_intronic(self, sv: hgvs.sequencevariant.SequenceVariant):
         """
         Checks if the given SequenceVariant is intronic.
@@ -71,13 +71,13 @@ def is_intronic(self, sv: hgvs.sequencevariant.SequenceVariant):
         if isinstance(sv.posedit.pos, hgvs.location.BaseOffsetInterval):
             return (sv.posedit.pos.start.is_intronic or sv.posedit.pos.end.is_intronic)
         return False
-    
+
 
     def get_edit_type(self, sv: hgvs.sequencevariant.SequenceVariant):
         if sv is None or sv.posedit is None or sv.posedit.edit is None:
             return None
         return sv.posedit.edit.type
-    
+
     def get_position_and_state(self, sv: hgvs.sequencevariant.SequenceVariant):
         """
         Get the details of a sequence variant.
@@ -150,14 +150,14 @@ def extract_allele_values(self, hgvs_expr: str):
         sv = self.parse(hgvs_expr)
         if not sv:
             return None
-        
+
         if self.is_intronic(sv):
             raise ValueError("Intronic HGVS variants are not supported")
 
         refget_accession = self.data_proxy.derive_refget_accession(sv.ac)
         if not refget_accession:
             return None
-        
+
         # translate coding coordinates to positional coordinates, if necessary
         if sv.type == "c":
             sv = self.c_to_n(sv)
@@ -166,7 +166,7 @@ def extract_allele_values(self, hgvs_expr: str):
 
         retval = {"refget_accession": refget_accession, "start": start, "end": end, "literal_sequence": state}
         return retval
-    
+
     def from_allele(self, vo, namespace=None):
         """generates a *list* of HGVS expressions for VRS Allele.
 
@@ -188,15 +188,15 @@ def from_allele(self, vo, namespace=None):
 
         if vo is None:
             return []
-        if not isinstance(vo, models.Allele): 
+        if not isinstance(vo, models.Allele):
             raise ValueError("VRS object must be an Allele")
         if vo.location is None:
             raise ValueError("VRS allele must have a location")
-        
+
         refget_accession = vo.location.get_refget_accession()
         if refget_accession is None:
             raise ValueError("VRS allele location must have a sequence reference")
-        
+
         sequence = f"ga4gh:{refget_accession}"
         aliases = self.data_proxy.translate_sequence_identifier(sequence, namespace)
 
@@ -218,9 +218,9 @@ def from_allele(self, vo, namespace=None):
             # create the hgvs expression object
             var = self._to_sequence_variant(vo, sequence_type, sequence, accession)
             hgvs_exprs += [str(var)]
-         
+
         return list(set(hgvs_exprs))
-    
+
     def _to_sequence_variant(self, vo, sequence_type, sequence, accession):
         """Creates a SequenceVariant object from an Allele object."""
           # build interval and edit depending on sequence type
@@ -253,24 +253,24 @@ def _to_sequence_variant(self, vo, sequence_type, sequence, accession):
             # this will subsequently be converted back to `c.` after hgvs normalization
             type='n' if sequence_type == 'c' else sequence_type,
             posedit=posedit)
-        
+
         try:
             # if the namespace is GRC, can't normalize, since hgvs can't deal with it
             parsed = self.parse(str(var))
             var = self.normalize(parsed)
-            
+
             # if sequence_type is coding, convert from "n." to "c." before continuing
             if sequence_type == "c":
                 var = self.n_to_c(var)
-            
+
         except hgvs.exceptions.HGVSDataNotAvailableError:
             _logger.warning(f"No data found for accession {accession}")
-        
+
         return var
 
     def normalize(self, hgvs):
         return self.normalizer.normalize(hgvs)
-    
+
     def n_to_c(self, hgvs):
         return self.variant_mapper.n_to_c(hgvs)
 
@@ -312,4 +312,3 @@ def c_to_n(self, hgvs):
     hgvs_expr = hgvsTools.from_allele(vrs_allele, namespace="refseq")
 
     print(hgvs_expr)
-

submodules/README.md

@@ -1,4 +1,3 @@
 This directory contains submodules required by vrs-python. If you
 don't see a vrs directory here, please reread instructions at
 https://github.com/ga4gh/vrs-python#installing-for-development.
-

tests/extras/data/test_vcf_input.vcf

@@ -235,4 +235,4 @@ chr19	28946400	.	T	C	50	PASS	platforms=5;platformnames=Illumina,PacBio,CG,10X,So
 chr19	490414	.	ACT	A	50	PASS	platforms=5;platformnames=Illumina,PacBio,CG,10X,Solid;datasets=5;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR,SolidSE75bp;callsets=7;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbDV,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,10XLRGATK,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CCS15kb_20kbDV_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;filt=CS_10XLRGATK_filt	GT:PS:DP:ADALL:AD:GQ	0/1:.:821:163,158:239,220:1004
 chr19	54220024	.	G	*,A	50	PASS	platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged	GT:PS:DP:ADALL:AD:GQ	1/2:.:45:0,20,25:0,20,25:99
 chr19	54220999	.	A	T	50	PASS	platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged	GT:PS:DP:ADALL:AD:GQ	0/1:.:45:0,20,25:0,20,25:99
-chr19	54221654	.	T	A,P	50	PASS	platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged	GT:PS:DP:ADALL:AD:GQ	0/1:.:45:0,20,25:0,20,25:99
+chr19	54221654	.	T	A,P	50	PASS	platforms=1;platformnames=PacBio;datasets=1;datasetnames=CCS15kb_20kb;callsets=1;callsetnames=CCS15kb_20kbGATK4;datasetsmissingcall=HiSeqPE300x,CCS15kb_20kb,10XChromiumLR,CGnormal,IonExome,SolidSE75bp;callable=CS_CCS15kb_20kbGATK4_callable;filt=CS_CCS15kb_20kbDV_filt,CS_10XLRGATK_filt,CS_HiSeqPE300xfreebayes_filt;difficultregion=HG001.hg38.300x.bam.bilkentuniv.010920.dups,hg38.segdups_sorted_merged	GT:PS:DP:ADALL:AD:GQ	0/1:.:45:0,20,25:0,20,25:99