From 78028affc20b95f18da4c5a92951631b14f43911 Mon Sep 17 00:00:00 2001 From: Per Unneberg Date: Wed, 9 Aug 2023 14:28:29 +0200 Subject: [PATCH 1/3] Elaborate installation docs --- .pre-commit-config.yaml | 14 +++++++------- README.md | 6 ++++++ docs/slides/genetic_diversity/index.qmd | 9 ++++++--- 3 files changed, 19 insertions(+), 10 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 70094e12..d2825aae 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: - id: check-yaml - id: trailing-whitespace - repo: https://github.com/asottile/reorder_python_imports - rev: v3.9.0 + rev: v3.10.0 hooks: - id: reorder-python-imports args: @@ -28,7 +28,7 @@ repos: --unclassifiable-application-module=_tskit, ] - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: "v0.0.262" + rev: "v0.0.282" hooks: - id: ruff args: @@ -36,19 +36,19 @@ repos: "--per-file-ignores=tests/test_utils.py:E501,manticore/tests/wm/snakemake.py:E501", ] - repo: https://github.com/psf/black - rev: 23.3.0 + rev: 23.7.0 hooks: - id: black language_version: python3 - repo: https://github.com/asottile/blacken-docs - rev: 1.13.0 + rev: 1.15.0 hooks: - id: blacken-docs args: [--skip-errors] additional_dependencies: [black==22.3.0] language_version: python3 - repo: https://github.com/DavidAnson/markdownlint-cli2 - rev: v0.7.0 + rev: v0.8.1 hooks: - id: markdownlint-cli2 files: \.(md|qmd)$ @@ -59,13 +59,13 @@ repos: types: [file] exclude: LICENSE.md - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: '2.7.1' + rev: '2.7.2' hooks: - id: editorconfig-checker alias: ec pass_filenames: true - repo: https://github.com/lorenzwalthert/precommit - rev: v0.3.2.9007 + rev: v0.3.2.9019 hooks: - id: style-files name: style-files diff --git a/README.md b/README.md index 8d4b2c96..59c31e5f 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,12 @@ environment variable: make install-bcftools make install-dev +If the above commands have worked without issues you are done and you +can head over to the section on [rendering documents](#Local +preview/render). If not, start by reading the following sections that +describe each installation step in more detail. There is also a +section on [known installation issues](#Installation issues). + ### Create pgip conda environment Create a conda environment called `pgip` using the environment file diff --git a/docs/slides/genetic_diversity/index.qmd b/docs/slides/genetic_diversity/index.qmd index c6d20a8e..6eda0b3c 100644 --- a/docs/slides/genetic_diversity/index.qmd +++ b/docs/slides/genetic_diversity/index.qmd @@ -47,7 +47,8 @@ passing here, and refer to section on demography later on. a rapid decrease of population size during last few generations will lead to significant reduction in heterozygosity. -Genetic diversity is not the only issue for conservation however [@lewis_BiggestEverStudy_2023]: +Genetic diversity is not the only issue for conservation however +[@lewis_BiggestEverStudy_2023]: >The analysis of all 233 species’ genomes also has implications for >conservation. For example, it shows that genetic diversity within a @@ -85,7 +86,8 @@ head(data) ::: {.notes } -Riddle: why is genetic diversity range so narrow? Possibly there are lower and upper limits. +Riddle: why is genetic diversity range so narrow? Possibly there are +lower and upper limits. Lower limit: censoring effect, i.e., when diversity passes a lower limit, population is driven to extinction due to inability to adapt @@ -101,7 +103,8 @@ selection; little support for this in literature. Purifying selection. Nearly neutral model could explain narrow range. [@ellegren_DeterminantsGeneticDiversity_2016] Upper limit could in -part be explained by linked selection [@corbett-detig_NaturalSelectionConstrains_2015] +part be explained by linked selection +[@corbett-detig_NaturalSelectionConstrains_2015] ::: From f06890d49d1f3a96cf4335125f67d7d85af59c6a Mon Sep 17 00:00:00 2001 From: Per Unneberg Date: Wed, 9 Aug 2023 15:04:59 +0200 Subject: [PATCH 2/3] Fix markdown links --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 59c31e5f..5414ab2d 100644 --- a/README.md +++ b/README.md @@ -28,10 +28,11 @@ environment variable: make install-dev If the above commands have worked without issues you are done and you -can head over to the section on [rendering documents](#Local -preview/render). If not, start by reading the following sections that -describe each installation step in more detail. There is also a -section on [known installation issues](#Installation issues). +can head over to the section on [rendering +documents](#local-preview/render). If not, start by reading the +following sections that describe each installation step in more +detail. There is also a section on [known installation +issues](#installation-issues). ### Create pgip conda environment From b9b423fd9799ea13d8f98ceb370719e0d2887576 Mon Sep 17 00:00:00 2001 From: Per Unneberg Date: Wed, 9 Aug 2023 15:41:20 +0200 Subject: [PATCH 3/3] Remove slash --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5414ab2d..3421b143 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ environment variable: If the above commands have worked without issues you are done and you can head over to the section on [rendering -documents](#local-preview/render). If not, start by reading the +documents](#local-previewrender). If not, start by reading the following sections that describe each installation step in more detail. There is also a section on [known installation issues](#installation-issues).