From c7049a0c6f23ce74fb36f27b0840257665d1f52e Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:21:49 +0100 Subject: [PATCH 1/7] purge table layout forcing to keep scrolleable tables --- docs/_static/fix_tables.css | 7 ------- docs/source/_templates/layout.html | 2 +- 2 files changed, 1 insertion(+), 8 deletions(-) delete mode 100644 docs/_static/fix_tables.css diff --git a/docs/_static/fix_tables.css b/docs/_static/fix_tables.css deleted file mode 100644 index 189a7c2a3..000000000 --- a/docs/_static/fix_tables.css +++ /dev/null @@ -1,7 +0,0 @@ -.wy-table-responsive table td { - white-space: normal !important; -} - -.wy-table-responsive { - overflow: visible !important; -} diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html index f6fc75ddd..32e730537 100644 --- a/docs/source/_templates/layout.html +++ b/docs/source/_templates/layout.html @@ -1,3 +1,3 @@ {% extends "!layout.html" %} {% set script_files = script_files + ["_static/welcome_owl.carousel.min.js"] %} -{% set css_files = css_files + ["_static/welcome_owl.carousel.css", "_static/welcome_owl.carousel.theme.css", "_static/fix_tables.css"] %} +{% set css_files = css_files + ["_static/welcome_owl.carousel.css", "_static/welcome_owl.carousel.theme.css"] %} From 23523e7c0e028800a99a7bab900812d31d5e389b Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:22:10 +0100 Subject: [PATCH 2/7] docs rtd theme to 2.0.0 --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 56d41a584..f330fe4e6 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ sphinx==7.2.6 mock==5.1.0 -sphinx_rtd_theme==1.3.0 +sphinx_rtd_theme==2.0.0 sphinx-argparse==0.4.0 \ No newline at end of file From 7cdab5604b0b1be23e91f0c691f3252946f0d358 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:23:33 +0100 Subject: [PATCH 3/7] include ESS for T2T + GRCz11, recheck khmer generated ones --- docs/content/feature/effectiveGenomeSize.rst | 80 +++++++++++++------- 1 file changed, 53 insertions(+), 27 deletions(-) diff --git a/docs/content/feature/effectiveGenomeSize.rst b/docs/content/feature/effectiveGenomeSize.rst index 4cbbb2dd5..e988b18e1 100644 --- a/docs/content/feature/effectiveGenomeSize.rst +++ b/docs/content/feature/effectiveGenomeSize.rst @@ -6,30 +6,56 @@ A number of tools can accept an "effective genome size". This is defined as the 1. The number of non-N bases in the genome. 2. The number of regions (of some size) in the genome that are uniquely mappable (possibly given some maximal edit distance). -Option 1 can be computed using ``faCount`` from `Kent's tools `__. The effective genome size for a number of genomes using this method is given below: - -======== ============== -Genome Effective size -======== ============== -GRCh37 2864785220 -GRCh38 2913022398 -GRCm37 2620345972 -GRCm38 2652783500 -dm3 162367812 -dm6 142573017 -GRCz10 1369631918 -WBcel235 100286401 -TAIR10 119481543 -======== ============== - -These values only appropriate if multimapping reads are included. If they are excluded (or there's any MAPQ filter applied), then values derived from option 2 are more appropriate. These are then based on the read length. We can approximate these values for various read lengths using the `khmer program `__ program and ``unique-kmers.py`` in particular. A table of effective genome sizes given a read length using this method is provided below: - -=========== ========== ========== ========== ========== ========= ========= ========== ======== -Read length GRCh37 GRCh38 GRCm37 GRCm38 dm3 dm6 GRCz10 WBcel235 -=========== ========== ========== ========== ========== ========= ========= ========== ======== -50 2685511504 2701495761 2304947926 2308125349 130428560 125464728 1195445591 95159452 -75 2736124973 2747877777 2404646224 2407883318 135004462 127324632 1251132686 96945445 -100 2776919808 2805636331 2462481010 2467481108 139647232 129789873 1280189044 98259998 -150 2827437033 2862010578 2489384235 2494787188 144307808 129941135 1312207169 98721253 -200 2855464000 2887553303 2513019276 2520869189 148524010 132509163 1321355241 98672758 -=========== ========== ========== ========== ========== ========= ========= ========== ======== +Option 1 can be computed using ``faCount`` from `Kents tools `__. +The effective genome size for a number of genomes using this method is given below: + + ++---------------+------------------+ +| Genome | Effective size | ++===============+==================+ +|GRCh37 | 2864785220 | ++---------------+------------------+ +|GRCh38 | 2913022398 | ++---------------+------------------+ +|T2T/CHM13CAT_v2| 3117292070 | ++---------------+------------------+ +|GRCm37 | 2620345972 | ++---------------+------------------+ +|GRCm38 | 2652783500 | ++---------------+------------------+ +|dm3 | 162367812 | ++---------------+------------------+ +|dm6 | 142573017 | ++---------------+------------------+ +|GRCz10 | 1369631918 | ++---------------+------------------+ +|GRCz11 | 1368780147 | ++---------------+------------------+ +|WBcel235 | 100286401 | ++---------------+------------------+ +|TAIR10 | 119482012 | ++---------------+------------------+ + + + +These values only appropriate if multimapping reads are included. If they are excluded (or there's any MAPQ filter applied), +then values derived from option 2 are more appropriate. +These are then based on the read length. +We can approximate these values for various read lengths using the `khmer program `__ program and ``unique-kmers.py`` in particular. +A table of effective genome sizes given a read length using this method is provided below: + ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|Read length | GRCh37 | GRCh38 | T2T/CHM13CAT_v2 | GRCm37 | GRCm38 | dm3 | dm6 | GRCz10 | GRCz11 | WBcel235 | TAIR10 | ++=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+ +|50 | 2685511454 | 2701495711 | 2725240337 | 2304947876 | 2308125299 | 130428510 | 125464678 | 1195445541 | 1197575653 | 95159402 | 114339094 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|75 | 2736124898 | 2747877702 | 2786136059 | 2404646149 | 2407883243 | 135004387 | 127324557 | 1251132611 | 1250812288 | 96945370 | 115317469 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|100 | 2776919708 | 2805636231 | 2814334875 | 2462480910 | 2467481008 | 139647132 | 129789773 | 1280188944 | 1280354977 | 98259898 | 118459858 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|150 | 2827436883 | 2862010428 | 2931551487 | 2489384085 | 2494787038 | 144307658 | 129940985 | 1312207019 | 1311832909 | 98721103 | 118504138 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|200 | 2855463800 | 2887553103 | 2936403235 | 2513019076 | 2520868989 | 148523810 | 132508963 | 1321355041 | 1322366338 | 98672558 | 117723393 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ +|250 | 2855044784 | 2898802627 | 2960856300 | 2528988583 | 2538590322 | 151901455 | 132900923 | 1339205109 | 1342093482 | 101271756 | 119585546 | ++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+ From 7b6a4339ab72e51c928cb920aee041d5b511977a Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:25:33 +0100 Subject: [PATCH 4/7] include doc changes in CHANGES --- CHANGES.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES.txt b/CHANGES.txt index f9bff7ab2..21ba877ea 100755 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -3,6 +3,7 @@ * doc fixes (argparse properly displayed, minor changes in installation instructions) * deepblue support stops * initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better). +* documentation changes to improve ESS tab, table constraints have been lifted & sphinx_rtd_theme to v2.0.0 3.5.4 * error handling and cases for bwAverage with >2 samples From 4c3545de934387d1a96cdd6d5fec5ad8f25ff101 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:41:49 +0100 Subject: [PATCH 5/7] revert back to upload_artifact v3 for now --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 182885b18..9bc28697b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -63,9 +63,9 @@ jobs: micromamba activate test_and_build rm -f dist/* python -m build - - uses: actions/upload-artifact@master + - uses: actions/upload-artifact@v3 with: - name: "Dist files" + name: "distfiles" path: "dist" test-wheels: name: test wheel From 11343cb765168b417f6f8f7cb7873bf0eb2a3519 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:46:02 +0100 Subject: [PATCH 6/7] namechange of artifact in test --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9bc28697b..07ffd664d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/download-artifact@v3 with: - name: "Dist files" + name: "distfiles" path: ~/dist/ - uses: actions/setup-python@v4 with: From 9dd5c031457a2b4591f302f0b4639c88651a790a Mon Sep 17 00:00:00 2001 From: WardDeb Date: Tue, 9 Jan 2024 17:51:27 +0100 Subject: [PATCH 7/7] pin upload artifact --- CHANGES.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES.txt b/CHANGES.txt index 21ba877ea..ea5b937c7 100755 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -4,6 +4,7 @@ * deepblue support stops * initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better). * documentation changes to improve ESS tab, table constraints have been lifted & sphinx_rtd_theme to v2.0.0 +* upload artifact in gh test runner pinned to 3 3.5.4 * error handling and cases for bwAverage with >2 samples