effective genome sizes in docs

.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
@@ -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:

CHANGES.txt

@@ -3,6 +3,8 @@
 * 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
+* upload artifact in gh test runner pinned to 3
 
 3.5.4
 * error handling and cases for bwAverage with >2 samples

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 <https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>`__. 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 <https://khmer.readthedocs.io/en/v2.1.1/>`__ 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 <https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>`__. 
+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 <https://khmer.readthedocs.io/en/latest/>`__ 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 |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+

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

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"] %}