gentroutils 3.0.0__tar.gz → 3.1.0__tar.gz

{gentroutils-3.0.0 → gentroutils-3.1.0}/.github/workflows/build.yaml

@@ -8,11 +8,12 @@ env:
   GCP_PROJECT_ID: "open-targets-genetics-dev"
   GCP_REGION: "europe-west1"
   TAG: "${{ github.ref_name }}"
-  REPO: "${{ github.event.repository_name }}"
+  REPO: "${{ github.event.repository.name }}"
 
 
 jobs:
   push-to-ghcr-and-gar:
+    if: startsWith(github.ref, 'refs/tags/')
     name: Build docker image and push to GHCR and GAR
     runs-on: ubuntu-22.04
 
@@ -54,7 +55,9 @@ jobs:
         name: Authenticate to Google Cloud
         uses: google-github-actions/auth@v2
         with:
+          token_format: access_token
           project_id: ${{ env.GCP_PROJECT_ID }}
+          service_account: github-actions@open-targets-genetics-dev.iam.gserviceaccount.com
           workload_identity_provider: projects/234703259993/locations/global/workloadIdentityPools/github/providers/opentargets
           access_token_lifetime: 300s
 
@@ -75,13 +78,13 @@ jobs:
           tags: |
             ghcr.io/${{ github.repository }}:latest
             ghcr.io/${{ github.repository }}:${{ env.TAG }}
-            ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/${{ env.REPO }}/${{ env.REPO }}:latest
-            ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/${{ env.REPO }}:${{ env.TAG }}
+            ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/opentargets/${{ env.REPO }}:latest
+            ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/opentargets/${{ env.REPO }}:${{ env.TAG }}
 
       - id: generate-attestations
         name: Generate artifact attestation
         uses: actions/attest-build-provenance@v1
         with:
-          subject-name: ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/${{ env.REPO }}/${{ env.REPO }}
+          subject-name: ${{ env.GCP_REGION }}-docker.pkg.dev/${{ env.GCP_PROJECT_ID }}/opentargets/${{ env.REPO }}
           subject-digest: ${{ steps.push.outputs.digest }}
           push-to-registry: true

{gentroutils-3.0.0 → gentroutils-3.1.0}/.github/workflows/tag.yaml

@@ -4,12 +4,16 @@ on:
     branches:
       - dev
       - main
+    tags-ignore: # Prevent running the action on the tag
+      - '*'
 
 
 jobs:
   create-tag:
-    # NOTE: only trigger the workflow when the commit is not from the GitHubActions bot (prevent self-triggering)
-    if: github.event.commits[0].author.name != 'github-actions[botg]'
+    # NOTE: only trigger the workflow only when human user pushed to the branch (prevent self-triggering)
+    if: |
+      !contains(fromJSON('["github-actions[bot]", "semantic-release"]'), github.actor) &&
+      github.event.head_commit.author.name != 'semantic-release'
     runs-on: ubuntu-latest
     concurrency: release
     environment: DEV

{gentroutils-3.0.0 → gentroutils-3.1.0}/CHANGELOG.md

@@ -1,6 +1,180 @@
 # CHANGELOG
 
 
+## v3.1.0 (2025-09-02)
+
+### Chores
+
+- Trigger release process ([#36](https://github.com/opentargets/gentroutils/pull/36),
+  [`a90fdc7`](https://github.com/opentargets/gentroutils/commit/a90fdc7cd26dcb1263590f93f79bff6ccc867868))
+
+* fix: update auth
+
+* 3.0.1-dev.1
+
+Automatically generated by python-semantic-release
+
+* ci: add service account to impersonate
+
+* 3.0.1-dev.2
+
+* ci: prevent running create-tag on tag
+
+* 3.0.1-dev.3
+
+* ci: prevent running create-tag by semantic-release
+
+* fix: workflow file
+
+* 3.0.1-dev.4
+
+* chore: update readme
+
+* ci: run artifact build only from tag
+
+* 3.0.1-dev.5
+
+* ci: prevent tag action to run after semvar
+
+* 3.0.1-dev.6
+
+* build: remove obscured gcs scope from polars
+
+* feat: rebuild docker image
+
+* feat: add docker build command
+
+* 3.1.0-dev.1
+
+* ci: fix container name
+
+* 3.1.0-dev.2
+
+* ci: change image name structure for gcs
+
+* 3.1.0-dev.3
+
+* ci: update path to attestations
+
+* 3.1.0-dev.4
+
+* 3.1.0-dev.5
+
+---------
+
+Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
+
+Co-authored-by: semantic-release <semantic-release>
+
+Co-authored-by: project-defiant <szymonszyszkowski@gmail.com>
+
+
+## v3.1.0-dev.5 (2025-08-29)
+
+### Continuous Integration
+
+- Update path to attestations
+  ([`febea43`](https://github.com/opentargets/gentroutils/commit/febea4366fe94de09b82154d92b90baadfb08871))
+
+
+## v3.1.0-dev.4 (2025-08-29)
+
+### Continuous Integration
+
+- Update path to attestations
+  ([`55a80f1`](https://github.com/opentargets/gentroutils/commit/55a80f11838d6569f4919b730e291be665f33dad))
+
+
+## v3.1.0-dev.3 (2025-08-29)
+
+### Continuous Integration
+
+- Change image name structure for gcs
+  ([`88dbbbd`](https://github.com/opentargets/gentroutils/commit/88dbbbd7637bf7c9ec8c405a9811ad9e29416d48))
+
+
+## v3.1.0-dev.2 (2025-08-29)
+
+### Continuous Integration
+
+- Fix container name
+  ([`9c64ae1`](https://github.com/opentargets/gentroutils/commit/9c64ae1e4d43b1861625ef673df8edd7b5127b48))
+
+
+## v3.1.0-dev.1 (2025-08-29)
+
+### Build System
+
+- Remove obscured gcs scope from polars
+  ([`895bfed`](https://github.com/opentargets/gentroutils/commit/895bfed2486c6ca5123cc6908760020d832638ec))
+
+### Features
+
+- Add docker build command
+  ([`8f42913`](https://github.com/opentargets/gentroutils/commit/8f42913c6c41b160a28ca230cb801dd2da0bebf1))
+
+- Rebuild docker image
+  ([`94f2a49`](https://github.com/opentargets/gentroutils/commit/94f2a49ccb25a8c9eb9238cd56ea75024e26ff50))
+
+
+## v3.0.1-dev.6 (2025-08-29)
+
+### Continuous Integration
+
+- Prevent tag action to run after semvar
+  ([`847e36b`](https://github.com/opentargets/gentroutils/commit/847e36ba4a5848116c2f6311849a1960dd55b34c))
+
+
+## v3.0.1-dev.5 (2025-08-29)
+
+### Chores
+
+- Update readme
+  ([`9e75c35`](https://github.com/opentargets/gentroutils/commit/9e75c35a4ed6113dae76ed9b0a67762fbcd882e3))
+
+### Continuous Integration
+
+- Run artifact build only from tag
+  ([`4906b38`](https://github.com/opentargets/gentroutils/commit/4906b38c49d51a7b8a6a28cb12638ecc9a6fdc5e))
+
+
+## v3.0.1-dev.4 (2025-08-29)
+
+### Bug Fixes
+
+- Workflow file
+  ([`f840d55`](https://github.com/opentargets/gentroutils/commit/f840d555bbf4a8415c71b56b34d72393af8c8ebf))
+
+### Continuous Integration
+
+- Prevent running create-tag by semantic-release
+  ([`57fb068`](https://github.com/opentargets/gentroutils/commit/57fb068a21bf86d048376ab0f4678694abeb2e71))
+
+
+## v3.0.1-dev.3 (2025-08-29)
+
+### Continuous Integration
+
+- Prevent running create-tag on tag
+  ([`963f657`](https://github.com/opentargets/gentroutils/commit/963f657221f2f08f20f1b20a371ad884d584bf0a))
+
+
+## v3.0.1-dev.2 (2025-08-29)
+
+### Continuous Integration
+
+- Add service account to impersonate
+  ([`05d5eb1`](https://github.com/opentargets/gentroutils/commit/05d5eb133efc9a5e3103397ff33233b543c1d2e2))
+
+
+## v3.0.1-dev.1 (2025-08-28)
+
+### Bug Fixes
+
+- Update auth
+  ([`a95b566`](https://github.com/opentargets/gentroutils/commit/a95b566a164d31ad36383fb99d7c88a5aec27b70))
+
+
 ## v3.0.0 (2025-08-28)
 
 ### Bug Fixes

gentroutils-3.1.0/Dockerfile

@@ -0,0 +1,29 @@
+# Description: Dockerfile for the gentroutils package
+#
+# To run locally, you must have a credentials file for GCP. Assuming you do,
+# you can run the following command:
+#
+# docker run -v /path/to/credentials.json:/app/credentials.json \
+#     -e GOOGLE_APPLICATION_CREDENTIALS=/app/credentials.json  \
+#     gentroutuls -s gwas_catalog_release
+# By default the image uses the `config.yaml` file provided in the repository.
+FROM rust:slim-trixie AS rust-builder
+FROM python:3.13.7-slim-trixie
+
+# Copy Rustc and Cargo from the rust-builder stage
+# These are needed to install polars without compiling rust from source
+COPY --from=rust-builder /usr/local/cargo/bin/rustc /usr/local/bin/rustc
+COPY --from=rust-builder /usr/local/cargo/bin/cargo /usr/local/bin/cargo
+
+# Copy Python source
+COPY src /app/src
+COPY pyproject.toml /app/pyproject.toml
+COPY uv.lock /app/uv.lock
+COPY README.md /app/README.md
+COPY config.yaml /app/config.yaml
+
+# Build the executable
+WORKDIR /app
+RUN python -m pip install .
+
+ENTRYPOINT [ "gentroutils", "-c", "/app/config.yaml" ]

{gentroutils-3.0.0 → gentroutils-3.1.0}/Makefile

@@ -1,6 +1,6 @@
 SHELL := /bin/bash
 .PHONY: $(shell sed -n -e '/^$$/ { n ; /^[^ .\#][^ ]*:/ { s/:.*$$// ; p ; } ; }' $(MAKEFILE_LIST))
-VERSION := $$(grep '^version' pyproject.toml | sed 's%version = "\(.*\)"%\1%')
+VERSION := $$(grep '^version' pyproject.toml | head -1 | sed 's%version = "\(.*\)"%\1%')
 APP_NAME := $$(grep '^name' pyproject.toml | head -1 | sed 's%name = "\(.*\)"%\1%')
 
 .DEFAULT_GOAL := help
@@ -41,3 +41,6 @@ check: lint format test type-check dep-check ## run all checks
 
 help: ## This is help
 	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+
+build-docker: ## build docker image
+	docker build -t $(APP_NAME):$(VERSION) --no-cache -f Dockerfile .

{gentroutils-3.0.0 → gentroutils-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gentroutils
-Version: 3.0.0
+Version: 3.1.0
 Summary: Open Targets python genetics utility CLI tools
 Author-email: Szymon Szyszkowski <ss60@sanger.ac.uk>
 License-Expression: Apache-2.0
@@ -19,7 +19,7 @@ Requires-Dist: gcsfs>=2025.7.0
 Requires-Dist: google-cloud-storage>=3.1.1
 Requires-Dist: loguru>=0.7.3
 Requires-Dist: opentargets-otter>=25.0.2
-Requires-Dist: polars[fsspec,gcs]>=1.31.0
+Requires-Dist: polars[fsspec]>=1.31.0
 Requires-Dist: pydantic>=2.10.6
 Requires-Dist: tqdm>=4.67.1
 Description-Content-Type: text/markdown
@@ -34,7 +34,7 @@ Set of Command Line Interface tools to process Open Targets Genetics GWAS data.
 
 ## Installation
 
-```
+```{bash}
 pip install gentroutils
 ```
 
@@ -121,7 +121,8 @@ The list of tasks (defined in the `config.yaml` file) that can be run are:
 
 This task fetches the latest GWAS Catalog release metadata from the `https://www.ebi.ac.uk/gwas/api/search/stats` endpoint and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE]
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `destination_template` is where the metadata will be saved, and it uses the `{release_date}` placeholder to specify the release date dynamically. By default it searches for the release directly in the stats_uri json output.
@@ -141,7 +142,8 @@ This task fetches the latest GWAS Catalog release metadata from the `https://www
 
 This task fetches the GWAS Catalog associations file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE]
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog associations file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.
@@ -162,7 +164,8 @@ This task fetches the GWAS Catalog associations file from the specified FTP serv
 
 This task fetches the GWAS Catalog studies file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE] 
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog studies file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.
@@ -183,7 +186,8 @@ This task fetches the GWAS Catalog studies file from the specified FTP server an
 
 This task fetches the GWAS Catalog ancestries file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE] 
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog ancestries file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.

{gentroutils-3.0.0 → gentroutils-3.1.0}/README.md

@@ -8,7 +8,7 @@ Set of Command Line Interface tools to process Open Targets Genetics GWAS data.
 
 ## Installation
 
-```
+```{bash}
 pip install gentroutils
 ```
 
@@ -95,7 +95,8 @@ The list of tasks (defined in the `config.yaml` file) that can be run are:
 
 This task fetches the latest GWAS Catalog release metadata from the `https://www.ebi.ac.uk/gwas/api/search/stats` endpoint and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE]
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `destination_template` is where the metadata will be saved, and it uses the `{release_date}` placeholder to specify the release date dynamically. By default it searches for the release directly in the stats_uri json output.
@@ -115,7 +116,8 @@ This task fetches the latest GWAS Catalog release metadata from the `https://www
 
 This task fetches the GWAS Catalog associations file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE]
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog associations file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.
@@ -136,7 +138,8 @@ This task fetches the GWAS Catalog associations file from the specified FTP serv
 
 This task fetches the GWAS Catalog studies file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE] 
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog studies file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.
@@ -157,7 +160,8 @@ This task fetches the GWAS Catalog studies file from the specified FTP server an
 
 This task fetches the GWAS Catalog ancestries file from the specified FTP server and saves it to the specified destination.
 
-> [!NOTE] > **Task parameters**
+> [!NOTE] 
+> **Task parameters**
 >
 > - The `stats_uri` is used to fetch the latest release date and other metadata.
 > - The `source_template` is the URL of the GWAS Catalog ancestries file, which uses the `{release_date}` placeholder to specify the release date dynamically. The release date is fetched from the `stats_uri` endpoint.

{gentroutils-3.0.0 → gentroutils-3.1.0}/pyproject.toml

@@ -1,12 +1,12 @@
 [project]
 authors = [{ name = "Szymon Szyszkowski", email = "ss60@sanger.ac.uk" }]
 name = "gentroutils"
-version = "3.0.0"
+version = "3.1.0"
 description = "Open Targets python genetics utility CLI tools"
 dependencies = [
     "aiohttp>=3.11.18",
     "aioftp>=0.25.1",
-    "polars[fsspec,gcs]>=1.31.0",
+    "polars[fsspec]>=1.31.0",
     "pydantic>=2.10.6",
     "loguru>=0.7.3",
     "tqdm>=4.67.1",

{gentroutils-3.0.0 → gentroutils-3.1.0}/uv.lock

@@ -500,7 +500,7 @@ wheels = [
 
 [[package]]
 name = "gentroutils"
-version = "3.0.0"
+version = "3.1.0"
 source = { editable = "." }
 dependencies = [
     { name = "aioftp" },
@@ -558,7 +558,7 @@ requires-dist = [
     { name = "google-cloud-storage", specifier = ">=3.1.1" },
     { name = "loguru", specifier = ">=0.7.3" },
     { name = "opentargets-otter", specifier = ">=25.0.2" },
-    { name = "polars", extras = ["fsspec", "gcs"], specifier = ">=1.31.0" },
+    { name = "polars", extras = ["fsspec"], specifier = ">=1.31.0" },
     { name = "pydantic", specifier = ">=2.10.6" },
     { name = "tqdm", specifier = ">=4.67.1" },
 ]

gentroutils-3.0.0/Dockerfile

@@ -1,16 +0,0 @@
-# Description: Dockerfile for the gentroutils package
-#
-# To run locally, you must have a credentials file for GCP. Assuming you do,
-# you can run the following command:
-#
-# docker run -v /path/to/credentials.json:/app/credentials.json -e GOOGLE_APPLICATION_CREDENTIALS=/app/credentials.json gentroutuls -s gwas_catalog_release
-
-FROM python:3.13.1-alpine3.21
-COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
-
-ADD . /app
-
-WORKDIR /app
-RUN uv sync --frozen
-
-ENTRYPOINT ["uv", "run", "gentroutils"]