From 9d971492ecf62d12ae62d04dd0e04b4505232afe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81ine=20O=27Toole?= Date: Thu, 30 Jun 2022 19:46:49 +0100 Subject: [PATCH 1/9] Update __init__.py --- pangolin/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pangolin/__init__.py b/pangolin/__init__.py index 01e6175..e18ab57 100644 --- a/pangolin/__init__.py +++ b/pangolin/__init__.py @@ -1,5 +1,5 @@ _program = "pangolin" -__version__ = "4.1" +__version__ = "4.1.1" __all__ = ["pangolearn", From 5eefe38e6cea08916acd22b7ea2d558ee25b218b Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Wed, 13 Jul 2022 10:21:55 +0200 Subject: [PATCH 2/9] Provide data packages compatibility list --- pangolin/data/data_compatibility.csv | 35 ++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 pangolin/data/data_compatibility.csv diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv new file mode 100644 index 0000000..73aae95 --- /dev/null +++ b/pangolin/data/data_compatibility.csv @@ -0,0 +1,35 @@ +data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.11,4, +pangolin-data,1.9,4, +pangolin-data,1.8,4, +pangolin-data,1.6,4, +pangolin-data,1.3,4, +pangolin-data,1.2.133,4, +pangolin-data,1.2.127,4, +pangolin-assignment,1.11,4, +pangolin-assignment,1.9,4, +pangolin-assignment,1.8,4, +pangolin-assignment,1.6,4, +pangolin-assignment,1.3,4, +pangolin-assignment,1.2.133,4, +constellations,0.1.10,,0.3.17 +constellations,0.1.9,,0.3.17 +constellations,0.1.8,,0.3.17 +constellations,0.1.7,,0.3.17 +constellations,0.1.6,,0.3.16 +constellations,0.1.5,,0.3.16 +constellations,0.1.4,,0.3.16 +constellations,0.1.3,,0.3.16 +constellations,0.1.2,,0.3.16 +constellations,0.1.1,,0.3.16 +constellations,0.1.0,,0.3.16 +constellations,0.0.30,,0.3.14 +constellations,0.0.29,,0.3.15 +constellations,0.0.28,,0.3.15 +constellations,0.0.27,,0.3.14 +constellations,0.0.26,,0.3.14 +constellations,0.0.25,,0.3.14 +constellations,0.0.24,,0.3.14 +constellations,0.0.23,,0.3.14 +constellations,0.0.22,,0.3.14 +constellations,0.0.21,,0.3.14 From a5ebeddba3925f7724f419604f79bfeafd080324 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81ine=20O=27Toole?= Date: Thu, 14 Jul 2022 10:10:14 +0100 Subject: [PATCH 3/9] Update pangolin.yml rm assignment cache use as it's failing from memory limitations --- .github/workflows/pangolin.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pangolin.yml b/.github/workflows/pangolin.yml index a1a1b6a..1de247c 100644 --- a/.github/workflows/pangolin.yml +++ b/.github/workflows/pangolin.yml @@ -55,8 +55,6 @@ jobs: run: pangolin --verbose pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_verbose.log - name: Add assignment cache run: pangolin --add-assignment-cache - - name: Test use-assignment-cache - run: pangolin --use-assignment-cache pangolin/test/test_seqs.fasta 2>&1 | grep 'Using pangolin-assignment cache' - name: remove assignment cache run: pip uninstall -y pangolin-assignment - name: Add assignment cache to datadir From e5e579e8339137e88785ff4c9134e36c05406d2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81ine=20O=27Toole?= Date: Thu, 14 Jul 2022 10:26:24 +0100 Subject: [PATCH 4/9] Update pangolin.yml rm datadir assignment cache ubuntu check for memory in actions reasons, still in mac test --- .github/workflows/pangolin.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/pangolin.yml b/.github/workflows/pangolin.yml index 1de247c..c0c1c1c 100644 --- a/.github/workflows/pangolin.yml +++ b/.github/workflows/pangolin.yml @@ -57,7 +57,3 @@ jobs: run: pangolin --add-assignment-cache - name: remove assignment cache run: pip uninstall -y pangolin-assignment - - name: Add assignment cache to datadir - run: mkdir ac && pangolin --add-assignment-cache --datadir ac - - name: Test use-assignment-cache with datadir - run: pangolin --use-assignment-cache --datadir ac pangolin/test/test_seqs.fasta 2>&1 | grep 'Using pangolin-assignment cache' From 827600237f82b267e29de33d92b26c59cf4f5d56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81ine=20O=27Toole?= Date: Thu, 14 Jul 2022 10:26:44 +0100 Subject: [PATCH 5/9] Update __init__.py --- pangolin/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pangolin/__init__.py b/pangolin/__init__.py index e18ab57..184df19 100644 --- a/pangolin/__init__.py +++ b/pangolin/__init__.py @@ -1,5 +1,5 @@ _program = "pangolin" -__version__ = "4.1.1" +__version__ = "4.1.2" __all__ = ["pangolearn", From 9f5015dcfaa620d911e2fc93e13a959561c982d9 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Mon, 18 Jul 2022 21:28:48 +0200 Subject: [PATCH 6/9] Add entry for pangolin-data / -assignment 1.12 (#476) Add an entry for pangolin-data / pangolin-assignment 1.12 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 73aae95..6b7c29a 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.12,4, pangolin-data,1.11,4, pangolin-data,1.9,4, pangolin-data,1.8,4, @@ -6,6 +7,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.12,4, pangolin-assignment,1.11,4, pangolin-assignment,1.9,4, pangolin-assignment,1.8,4, From a85856bf4dbb128d8070c2557da18c2ab1b3686b Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Wed, 10 Aug 2022 13:06:52 -0700 Subject: [PATCH 7/9] Add entries for pangolin-data/-assignment 1.13 (#479) (#480) --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 6b7c29a..ce1ea61 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.13,4, pangolin-data,1.12,4, pangolin-data,1.11,4, pangolin-data,1.9,4, @@ -7,6 +8,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.13,4, pangolin-assignment,1.12,4, pangolin-assignment,1.11,4, pangolin-assignment,1.9,4, From d640422bb945ea4c6e9ad7397d650a51474226fc Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Tue, 13 Sep 2022 10:51:13 -0700 Subject: [PATCH 8/9] Add entries for pangolin-data/-assignment 1.14 (#483) (#486) --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index ce1ea61..c947c97 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.14,4, pangolin-data,1.13,4, pangolin-data,1.12,4, pangolin-data,1.11,4, @@ -8,6 +9,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.14,4, pangolin-assignment,1.13,4, pangolin-assignment,1.12,4, pangolin-assignment,1.11,4, From 9e6ee9aee5d70fbebad919fc795669124eb38c71 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Mon, 10 Oct 2022 20:36:47 -0700 Subject: [PATCH 9/9] Add entries for pangolin-data/-assignment 1.15.1 (#488) (#490) --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index c947c97..6afcf8e 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.15.1,4, pangolin-data,1.14,4, pangolin-data,1.13,4, pangolin-data,1.12,4, @@ -9,6 +10,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.15.1,4, pangolin-assignment,1.14,4, pangolin-assignment,1.13,4, pangolin-assignment,1.12,4,