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Merge pull request #1504 from nextstrain/docs/improved
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@ivan-aksamentov
ivan-aksamentov authored Jul 4, 2024
2 parents ada3d80 + 30e7cce commit 518fe3d
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Showing 6 changed files with 36 additions and 12 deletions.
1 change: 1 addition & 0 deletions Makefile
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Expand Up @@ -77,5 +77,6 @@ docker-paper-preprint:
--volume="$(shell pwd):/home/user/src" \
--workdir="/home/user/src" \
--env "TERM=xterm-256colors" \
--ulimit core=0 \
"$${CONTAINER_IMAGE_NAME}" \
bash -c "make paper-preprint"
9 changes: 6 additions & 3 deletions docs/Makefile
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Expand Up @@ -16,11 +16,14 @@ help:

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
%: Makefile clean
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

autobuild:
sphinx-autobuild --host=0.0.0.0 --port=8000 . build/html
autobuild: clean
sphinx-autobuild --host=0.0.0.0 --port=8000 "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

linkcheck:
sphinx-build -b linkcheck $(SOURCEDIR) $(BUILDDIR)/linkcheck $(SPHINXOPTS) $(O)

clean:
rm -rf "$(BUILDDIR)"
10 changes: 10 additions & 0 deletions docs/_static/css/custom.css
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Expand Up @@ -26,3 +26,13 @@ details pre * {
.rst-content code {
font-size: 0.8em !important;
}

table {
table-layout: fixed !important;
}

th, td {
word-wrap: break-word !important;
white-space: normal !important;
}

10 changes: 10 additions & 0 deletions docs/conf.py
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Expand Up @@ -96,3 +96,13 @@

intersphinx_mapping = {
}


# Force full rebuild, including updating static files (such as custom css)
# https://github.com/sphinx-doc/sphinx/issues/2090#issuecomment-572902572
def env_get_outdated(app, env, added, changed, removed):
return ['index']


def setup(app):
app.connect('env-get-outdated', env_get_outdated)
16 changes: 8 additions & 8 deletions docs/user/output-files/04-results-tsv.md
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Expand Up @@ -25,7 +25,7 @@ Every row in tabular output corresponds to 1 input sequence. The meaning of colu
| seqName | Name of the sequence (as provided in the input file) | string | hCoV-19/USA/SEARCH-4652-SAN/2020 |
| clade | Assigned clade | string | 20A |
| qc.overallScore | Overall [quality control](../algorithm/07-quality-control) score | float | 23.5 |
| qc.overallStatus | Overall [quality control](../algorithm/07-quality-control) status | string: `good\|mediocre\|bad` | mediocre |
| qc.overallStatus | Overall [quality control](../algorithm/07-quality-control) status | string: `good | mediocre |bad` | mediocre |
| totalSubstitutions | Total number of detected nucleotide substitutions | non-negative integer | 2 |
| totalDeletions | Total number of deleted nucleotide bases | non-negative integer | 15 |
| totalInsertions | Total number of inserted nucleotide bases | non-negative integer | 3 |
Expand Down Expand Up @@ -75,31 +75,31 @@ Every row in tabular output corresponds to 1 input sequence. The meaning of colu
| relativeMutations\['<search.name\>'\].aaDeletions | List of detected aminoacid deletions relative to the node of interest | comma separated list of strings | N:E31-,N:E32- |
| qc.missingData.missingDataThreshold | Threshold that was used for "Missing data" QC rule | int | 3000 |
| qc.missingData.score | Score for "Missing data" QC rule | float | 0.5 |
| qc.missingData.status | Status for "Missing data" QC rule | string: `good\|mediocre\|bad` | mediocre |
| qc.missingData.status | Status for "Missing data" QC rule | string: `good | mediocre |bad` | mediocre |
| qc.missingData.totalMissing | Total number of missing nucleotides used in "Missing data" QC rule | non-negative integer | 238 |
| qc.mixedSites.mixedSitesThreshold | Threshold used for "Mixed sites" QC rule | int | 10 |
| qc.mixedSites.score | Score for "Mixed sites" QC rule | float | 0.5 |
| qc.mixedSites.status | Status for "Mixed sites" QC rule | string: `good\|mediocre\|bad` | good |
| qc.mixedSites.status | Status for "Mixed sites" QC rule | string: `good | mediocre |bad` | good |
| qc.mixedSites.totalMixedSites | Total number of ambiguous nucleotides used for "Mixed sites" QC rule | non-negative integer | 2 |
| qc.privateMutations.cutoff | Cutoff parameter used for "Private mutations" QC rule | int | 3 |
| qc.privateMutations.excess | Excess parameter used for "Private mutations" QC rule | int | 1 |
| qc.privateMutations.score | Score for "Private mutations" QC rule | float | 0.5 |
| qc.privateMutations.status | Status for "Private mutations" QC rule | string: `good\|mediocre\|bad` | good |
| qc.privateMutations.status | Status for "Private mutations" QC rule | string: `good | mediocre |bad` | good |
| qc.privateMutations.total | Weighted sum of private mutations used for "Private mutations" QC rule | non-negative integer | 4 |
| qc.snpClusters.clusteredSNPs | Clustered SNP detected for "SNP clusters" QC rule | comma separated list of strings | C241T,C2061T |
| qc.snpClusters.score | Score for "SNP clusters" QC rule | float | 0.5 |
| qc.snpClusters.status | Status for "SNP clusters" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.snpClusters.status | Status for "SNP clusters" QC rule | string: `good | mediocre |bad` | bad |
| qc.snpClusters.totalSNPs | Total number of SNPs for "SNP clusters" QC rule | non-negative integer | 2 |
| qc.frameShifts.frameShifts | List of detected frame shifts in "Frame shifts" QC rule (excluding ignored) | comma separated list of strings | N:33-420 |
| qc.frameShifts.totalFrameShifts | Total number of detected frame shifts in for "Frame shifts" QC rule (excluding ignored) | non-negative integer | 1 |
| qc.frameShifts.frameShiftsIgnored | List of frame shifts detected, but ignored due to ignore list | comma separated list of strings | ORF8:109-111 |
| qc.frameShifts.totalFrameShiftsIgnored | Total number of frame shifts detected, but ignored due to ignore list | non-negative integer | 1 |
| qc.frameShifts.score | Score for "Frame shifts" QC rule | float | 0.5 |
| qc.frameShifts.status | Status for "Frame shifts" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.frameShifts.status | Status for "Frame shifts" QC rule | string: `good | mediocre |bad` | bad |
| qc.stopCodons.stopCodons | List of detected stop codons in "Stop codons" QC rule | comma separated list of strings | ORF1a:4715,ORF1a:4716 |
| qc.stopCodons.totalStopCodons | Total number of detected stop codons in "Stop codons" QC rule | non-negative integer | 2 |
| qc.stopCodons.score | Score for "Stop codons" QC rule | float | 0.5 |
| qc.stopCodons.status | Status for "Stop codons" QC rule | string: `good\|mediocre\|bad` | bad |
| qc.stopCodons.status | Status for "Stop codons" QC rule | string: `good | mediocre |bad` | bad |
| isReverseComplement | Whether query sequences were transformed using reverse complement operation before alignment | boolean | false |
| errors | List of errors during processing | comma separated list of strings | |
| warnings | List of warnings during processing | comma separated list of strings | |
Expand All @@ -118,7 +118,7 @@ The table can contain additional columns for every clade-like attribute defined
>
> <br/>
>
> Care should be taken to check for `errors`, `warnings` and `failedCdses` columns or fields, to avoid treating missing or empty entries incorrectly. For example if and `errors` column is non-empty in the TSV output file, it means that the sequence processing failed completely, and treating the empty `substitutions` column as if no mutations detected is incorrect.
> Care should be taken to check for `errors`, `warnings` and `failedCdses` columns or fields, to avoid treating missing or empty entries incorrectly. For example if an `errors` column is non-empty in the TSV output file, it means that the sequence processing failed completely, and treating the empty `substitutions` column as if no mutations detected is incorrect.
>
> <br/>
>
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2 changes: 1 addition & 1 deletion docs/user/output-files/05-results-json.md
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Expand Up @@ -30,7 +30,7 @@ NDJSON file (newline-delimited JSON) combines only `results` and `errors` arrays
>
> <br/>
>
> Care should be taken to check for `errors`, `warnings` and `failedCdses` columns or fields, to avoid treating missing or empty entries incorrectly. For example if and `errors` column is non-empty in the TSV output file, it means that the sequence processing failed completely, and treating the empty `substitutions` column as if no mutations detected is incorrect.
> Care should be taken to check for `errors`, `warnings` and `failedCdses` columns or fields, to avoid treating missing or empty entries incorrectly. For example if an `errors` column is non-empty in the TSV output file, it means that the sequence processing failed completely, and treating the empty `substitutions` column as if no mutations detected is incorrect.
>
> <br/>
>
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