Merge pull request #23 from metagenlab/dev

update workflows and bump tool versions
metagenlab · Oct 22, 2024 · 22f4331 · 22f4331
2 parents 2ee35ae + e1765d3
commit 22f4331
Show file tree

Hide file tree

Showing 12 changed files with 33 additions and 43 deletions.
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -6,6 +6,14 @@ on:
     paths:
       - ".github/workflows/build-docs.yml"
       - "docs/**"
+      - "mkdocs.yml"
+      - "!Dockerfile"
+      - "!.github/workflows/docker-publish.yml"
+      - "!.github/workflows/unit-tests.yml"
+      - "!tests/**"
+      - "!assembly_finder/**"
+      - "!setup.py"
+      - "!README.md"
 
 # Cancel if a newer run is started
 concurrency:

diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -4,11 +4,14 @@ on:
   push:
     branches: [main]
     paths:
-    - "Dockerfile"
-    - ".github/workflows/docker-publish.yml"
-    - "tests/**"
-    - "assembly_finder/**"
-    - "setup.py"
+      - "Dockerfile"
+      - ".github/workflows/docker-publish.yml"
+      - "tests/**"
+      - "assembly_finder/**"
+      - "setup.py"
+      - "!docs/**"
+      - "!README.md"
+      - "!mkdocs.yml"
   release:
     types: [published]
 
@@ -54,4 +57,4 @@ jobs:
           push: true
           tags: |
             ghcr.io/metagenlab/assembly_finder:${{ github.event.release.tag_name }}
-            ghcr.io/metagenlab/assembly_finder:latest
+            ghcr.io/metagenlab/assembly_finder:latest
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -2,19 +2,15 @@ name: Tests
 
 on:
   push:
-    branches: ["main"]
-    paths:
-      - ".github/workflows/unit-tests.yml"
-      - "tests/**"
-      - "assembly_finder/**"
-      - "setup.py"
-  pull_request:
-    branches: ["main"]
+    branches: ["main","dev"]
     paths:
       - ".github/workflows/unit-tests.yml"
       - "tests/**"
       - "assembly_finder/**"
       - "setup.py"
+      - "!.github/workflows/build-docs.yml"
+      - "!docs/**"
+      - "!mkdocs.yml"
 
 permissions:
   contents: read

diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ tests/__pycache__
 taxons/
 .snakemake
 .taxonkit/
+test_out/
diff --git a/assembly_finder/__main__.py b/assembly_finder/__main__.py
@@ -132,7 +132,6 @@ def common_options(func):
                 "--output",
                 "--taxonkit",
                 "--threads",
-                "--requests",
                 "--taxon",
                 "--rank",
                 "--nrank",
@@ -206,13 +205,6 @@ def common_options(func):
     default=None,
 )
 @click.option("--api-key", type=str, help="NCBI api-key", default=None)
-@click.option(
-    "--requests",
-    type=int,
-    help="Number of NCBI datasets commands to run in parallel",
-    default=1,
-    show_default=True,
-)
 @click.option(
     "--compressed",
     type=bool,
@@ -257,7 +249,7 @@ def common_options(func):
 @click.option(
     "--annotated",
     type=bool,
-    help="Select annotated genomes only",
+    help="Limit to annotated genomes only",
     default=False,
     show_default=True,
 )

diff --git a/assembly_finder/assembly_finder.LICENSE b/assembly_finder/assembly_finder.LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024, Farid Chaabane
+Copyright (c) 2024, metagenlab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/assembly_finder/assembly_finder.VERSION b/assembly_finder/assembly_finder.VERSION
@@ -1 +1 @@
-0.7.7
+0.8.0
diff --git a/assembly_finder/config/config.yaml b/assembly_finder/config/config.yaml
@@ -17,7 +17,6 @@ args:
   profile:
   rank:
   reference:
-  requests:
   snake_args:
   snake_default:
   source:

diff --git a/assembly_finder/workflow/envs/datasets.yml b/assembly_finder/workflow/envs/datasets.yml
@@ -3,5 +3,4 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - ncbi-datasets-cli =16.26.2
-  - ca-certificates
+  - ncbi-datasets-cli =16.31.0
diff --git a/assembly_finder/workflow/rules/download.smk b/assembly_finder/workflow/rules/download.smk
@@ -43,8 +43,6 @@ if TAXON:
             limit=lambda wildcards: get_limit(wildcards, LIMIT, QUERY2NB),
             args=ARGS,
             key=KEY,
-        resources:
-            ncbi_requests=1,
         retries: 2
         conda:
             os.path.join(dir.env, "datasets.yml")
@@ -101,8 +99,6 @@ else:
         params:
             args=ARGS,
             key=KEY,
-        resources:
-            ncbi_requests=1,
         conda:
             os.path.join(dir.env, "datasets.yml")
         shell:
@@ -140,8 +136,6 @@ rule taxonkit_lineage:
     params:
         headers=config.headers.lineage,
         dir=TAXONKIT,
-    resources:
-        ncbi_requests=1,
     conda:
         os.path.join(dir.env, "taxonkit.yml")
     shell:
@@ -161,8 +155,6 @@ rule format_taxonkit_lineage:
     params:
         headers=config.headers.lineage,
         dir=TAXONKIT,
-    resources:
-        ncbi_requests=1,
     conda:
         os.path.join(dir.env, "csvtk.yml")
     shell:

diff --git a/env.yaml b/env.yaml
@@ -3,14 +3,14 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - ncbi-datasets-cli =16.26.2
+  - ncbi-datasets-cli =16.31.0
   - taxonkit =0.17.0
   - csvtk =0.30.0
   - python =3.12
   - pip
-  - snakemake-minimal =8.18.1
-  - snaketool-utils =0.0.5
+  - snakemake-minimal =8.23.1
+  - snaketool-utils =0.0.6
   - attrmap =0.0.7
-  - pyyaml =6.0
-  - pandas =2.2.1
-  - rich-click =1.7.4
+  - pyyaml =6.0.1
+  - pandas =2.2.3
+  - rich-click =1.8.3
diff --git a/setup.py b/setup.py
@@ -56,7 +56,7 @@ def get_data_files():
         "attrmap>=0.0.7",
         "pyyaml>=6.0",
         "pandas>=2.2.1",
-        "rich-click>=1.7.4",
+        "rich-click>=1.8.3",
     ],
     entry_points={"console_scripts": ["assembly_finder=assembly_finder.__main__:main"]},
     include_package_data=True,