From 62263b5ca6d7722b0469c7728b4c5d37b2329ffb Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:09:11 +0200
Subject: [PATCH 01/12] started ignoring test_out

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 66ffb4c..f2cd927 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ tests/__pycache__
 taxons/
 .snakemake
 .taxonkit/
+test_out/

From 0daadd340ca23fc9622fd8254a7bfe6aa1461dcb Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:09:23 +0200
Subject: [PATCH 02/12] bumped versions

---
 env.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/env.yaml b/env.yaml
index af17bf4..26fe6da 100644
--- a/env.yaml
+++ b/env.yaml
@@ -3,7 +3,7 @@ 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
@@ -11,6 +11,6 @@ dependencies:
   - snakemake-minimal =8.18.1
   - snaketool-utils =0.0.5
   - attrmap =0.0.7
-  - pyyaml =6.0
+  - pyyaml =6.0.1
   - pandas =2.2.1
-  - rich-click =1.7.4
+  - rich-click =1.8.3

From 4d73dc8a8083a64820b7a18afd8a6c132541fbc9 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:09:32 +0200
Subject: [PATCH 03/12] bumped rich-click version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d3ba888..ed26ea8 100644
--- 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,

From fdf509e5369f83856f18013cb6e658d3aaa69ecf Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:09:50 +0200
Subject: [PATCH 04/12] removed unused requests arg

---
 assembly_finder/__main__.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/assembly_finder/__main__.py b/assembly_finder/__main__.py
index 29104bf..d774562 100644
--- 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,
 )

From 1a7446a6e2c280b4c24140bae16bb2a1babda893 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:09:57 +0200
Subject: [PATCH 05/12] fixed license

---
 assembly_finder/assembly_finder.LICENSE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assembly_finder/assembly_finder.LICENSE b/assembly_finder/assembly_finder.LICENSE
index e6acd5f..b9e463f 100644
--- 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

From d353f3756c3860078bfdcd98825cd371ed94aa9e Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:10:03 +0200
Subject: [PATCH 06/12] bumped version

---
 assembly_finder/assembly_finder.VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assembly_finder/assembly_finder.VERSION b/assembly_finder/assembly_finder.VERSION
index 11d9d6c..8adc70f 100644
--- a/assembly_finder/assembly_finder.VERSION
+++ b/assembly_finder/assembly_finder.VERSION
@@ -1 +1 @@
-0.7.7
\ No newline at end of file
+0.8.0
\ No newline at end of file

From c07598c207d0673522526e0782fbe46496c573c0 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:10:12 +0200
Subject: [PATCH 07/12] updated config

---
 assembly_finder/config/config.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/assembly_finder/config/config.yaml b/assembly_finder/config/config.yaml
index e34f131..bb62370 100644
--- 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:

From 9fb4f55f878041a7be5471015d4b84f51f30b97f Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:10:22 +0200
Subject: [PATCH 08/12] bumped datasets version

---
 assembly_finder/workflow/envs/datasets.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/assembly_finder/workflow/envs/datasets.yml b/assembly_finder/workflow/envs/datasets.yml
index adf6f5b..9544e64 100644
--- 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

From 1f00877c4b681842d2f6885927515388f714e147 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:10:39 +0200
Subject: [PATCH 09/12] removed unused requests params

---
 assembly_finder/workflow/rules/download.smk | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/assembly_finder/workflow/rules/download.smk b/assembly_finder/workflow/rules/download.smk
index 5cbe326..4165e99 100644
--- 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:

From 39deec47a81cef4bfc27dc1d6a1a3c17319f2fa8 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:23:46 +0200
Subject: [PATCH 10/12] added paths ignore

---
 .github/workflows/build-docs.yml     |  8 ++++++++
 .github/workflows/docker-publish.yml | 15 +++++++++------
 .github/workflows/unit-tests.yml     | 10 +++-------
 3 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 329ad1f..11add64 100644
--- 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
index 394d74b..0e74b82 100644
--- 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
\ No newline at end of file
+            ghcr.io/metagenlab/assembly_finder:latest
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
index 10ca602..819dc1a 100644
--- a/.github/workflows/unit-tests.yml
+++ b/.github/workflows/unit-tests.yml
@@ -8,13 +8,9 @@ on:
       - "tests/**"
       - "assembly_finder/**"
       - "setup.py"
-  pull_request:
-    branches: ["main"]
-    paths:
-      - ".github/workflows/unit-tests.yml"
-      - "tests/**"
-      - "assembly_finder/**"
-      - "setup.py"
+      - "!.github/workflows/build-docs.yml"
+      - "!docs/**"
+      - "!mkdocs.yml"
 
 permissions:
   contents: read

From f2b9d9927cf77bc0b83c536384fa82affcb19cfb Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Thu, 17 Oct 2024 12:46:33 +0200
Subject: [PATCH 11/12] bumped versions

---
 env.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/env.yaml b/env.yaml
index 26fe6da..0015800 100644
--- a/env.yaml
+++ b/env.yaml
@@ -8,9 +8,9 @@ dependencies:
   - 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 =6.0.1
-  - pandas =2.2.1
+  - pandas =2.2.3
   - rich-click =1.8.3

From e1765d36b16a8cebe38d2f539d98e792038b00c6 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Tue, 22 Oct 2024 12:50:47 +0200
Subject: [PATCH 12/12] added dev branch

---
 .github/workflows/unit-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
index 819dc1a..70bccc9 100644
--- a/.github/workflows/unit-tests.yml
+++ b/.github/workflows/unit-tests.yml
@@ -2,7 +2,7 @@ name: Tests
 
 on:
   push:
-    branches: ["main"]
+    branches: ["main","dev"]
     paths:
       - ".github/workflows/unit-tests.yml"
       - "tests/**"