pints 1.1.13 (#6709)

* build(pints): Switch to PyPI The bioconda builds aren't getting updated, and the biocontainers containers aren't getting updated. They're publishing to PyPI consistently, so we'll meet them where they're at. Really need the stuff in hyulab/PINTS@101c0cb like yesterday. * chore: Add renovate comment * build: Include pybedtools manually And htslib for bgzip. pybedtools wiht pip needs gcc to install. * chore: Copy code from @ewels #6694 (comment) Co-authored-by: ewels <[email protected]> * build: Fix uv shebang * fix(#6694): Remove async code * style: Run ruff * fix(#6694): Clean up some errors And by that I mean comment out the code. Seriously anyone reading these? * chore: Clean up httpx * refactor: Simplify script * fix: Remove oras * fix: containerimage => containerImage * fix: Remove oras and mediatype => mediaType * style: Run ruff --------- Co-authored-by: ewels <[email protected]>
nf-core · Oct 3, 2024 · ac55541 · ac55541
1 parent f351fad
commit ac55541
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Showing 5 changed files with 96 additions and 13 deletions.
diff --git a/.github/scripts/wave_singularity.py b/.github/scripts/wave_singularity.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env -S uv run
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "httpx",
+# ]
+# ///
+
+import logging
+
+import httpx
+
+logger = logging.getLogger(__name__)
+
+image_url = "oras://community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:aa20de1f1b5ddb30"
+
+if image_url.startswith("oras://"):
+    image_url = image_url.replace("oras://", "")
+
+wave_api_url = "https://wave.seqera.io"
+url = f"{wave_api_url}/v1alpha1/inspect"
+
+# if platform_pat:
+#     data["toweraccesstoken"] = platform_pat
+# else:
+# TODO
+logger.warning("'platform_pat' not set, no auth to wave back end")
+
+try:
+    logger.info(f"calling image inspect at {url} for image url {image_url}")
+    response = httpx.post(
+        url=url,
+        json={"containerImage": image_url},
+        headers={"content-type": "application/json"},
+    )
+
+    data = response.json()
+    logger.debug(data)
+    layers = data.get("container", {}).get("manifest", {}).get("layers", [])
+    is_singularity = len(layers) == 1 and layers[0].get("mediaType", "").endswith(".sif")
+    if not is_singularity:
+        print(layers)
+        raise ValueError("not a singularity image")
+    if "digest" not in layers[0]:
+        print(layers)
+        raise ValueError("no 'digest' in first layer found")
+
+    digest = layers[0]["digest"].replace("sha256:", "")
+    container_url = f"https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/{digest[:2]}/{digest}/data"
+    print(container_url)
+
+except httpx.RequestError as exc:
+    print(f"An error occurred while requesting {exc.request.url!r}.")
+    print("No singularity image for you")
diff --git a/modules/nf-core/pints/caller/environment.yml b/modules/nf-core/pints/caller/environment.yml
@@ -2,4 +2,11 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pypints=1.1.10
+  - pybedtools
+  - bedtools
+  - htslib
+  - pip
+  - pip: # FIXME https://github.com/nf-core/modules/issues/5814
+      # NOTE PINTS isn't adding conda builds and is a few versions behind.
+      # renovate: datasource=pypi depName=pypints
+      - pypints==1.1.13
diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf
@@ -5,8 +5,8 @@ process PINTS_CALLER {
     conda "${moduleDir}/environment.yml"
     // NOTE Stopped publishing at 1.1.9 https://quay.io/repository/biocontainers/pypints?tab=tags
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pints_caller:650ef63c9768bb5a' :
-        'community.wave.seqera.io/library/pints_caller:b1e6404513917871' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f1a9e30012e1b41baf9acd1ff94e01161138d8aa17f4e97aa32f2dc4effafcd1/data' :
+        'community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:39699b96998ec5f6' }"
 
     input:
     tuple val(meta), path(bams), path(bais)

diff --git a/modules/nf-core/pints/caller/tests/main.nf.test b/modules/nf-core/pints/caller/tests/main.nf.test
@@ -35,7 +35,7 @@ nextflow_process {
                     process.out.divergent_TREs,
                     process.out.bidirectional_TREs,
                     file(process.out.unidirectional_TREs.get(0).get(1).get(0)).name,
-                    process.out.versions,
+                    path(process.out.versions.get(0)).yaml,
                 ).match("bams")
                 },
             )
@@ -65,9 +65,10 @@ nextflow_process {
                     process.out.divergent_TREs,
                     process.out.bidirectional_TREs,
                     file(process.out.unidirectional_TREs[0][1]).name,
-                    process.out.versions,
+                    path(process.out.versions.get(0)).yaml,
                 ).match("single_bam")
                 },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
             )
         }
     }

diff --git a/modules/nf-core/pints/caller/tests/main.nf.test.snap b/modules/nf-core/pints/caller/tests/main.nf.test.snap
@@ -1,4 +1,19 @@
 {
+    "versions": {
+        "content": [
+            {
+                "PINTS_CALLER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-29T22:22:29.559913"
+    },
     "bams": {
         "content": [
             [
@@ -24,15 +39,18 @@
                 ]
             ],
             "test_1_unidirectional_peaks.bed",
-            [
-                "versions.yml:md5,6142633d4306c8a74b9716c4aac7e956"
-            ]
+            {
+                "PINTS_CALLER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                }
+            }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T12:17:21.517020581"
+        "timestamp": "2024-09-29T22:19:23.738834"
     },
     "single_bam": {
         "content": [
@@ -55,14 +73,17 @@
                 ]
             ],
             "test_1_unidirectional_peaks.bed",
-            [
-                "versions.yml:md5,6142633d4306c8a74b9716c4aac7e956"
-            ]
+            {
+                "PINTS_CALLER": {
+                    "python": "3.12.6",
+                    "pints": "1.1.13"
+                }
+            }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:07:12.112579276"
+        "timestamp": "2024-09-29T22:22:29.544608"
     }
 }