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Merged
alpae merged 13 commits into from
Nov 4, 2026
+7,393 −68
Merged

Test suite ahead of the ete3 → ete4 migration #112

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200f4b9
test: add pytest infrastructure and run python tests in CI
alpae Oct 20, 2026
76034dd
test(nf-test): snapshot the inferred orthology instead of line counts
alpae Oct 20, 2026
b008a62
test(nf-test): cover id transformer, MSA/tree output, score flags, ar…
alpae Oct 20, 2026
945c03b
test: unit and stage tests for rootHOG inference, input checks and ba…
alpae Oct 20, 2026
3cce4f2
test: unit tests for collect-subhogs, pairwise relations, id transfor…
alpae Oct 20, 2026
5127475
chore: ignore nf-test working files
alpae Oct 20, 2026
c1040c9
test: unit and property tests for subHOG inference
alpae Oct 20, 2026
de46004
test: golden snapshots and no-dropped-protein checks on fungi-30 root…
alpae Nov 4, 2026
7abe2dc
test(nf-test): rebuild input archive without macOS AppleDouble files
alpae Nov 4, 2026
8c47c7e
test: pin hidden files in input folders being taken as proteomes/hogmaps
alpae Nov 4, 2026
bdb1b46
test: pin ImpliedLosses counting losses for complete HOGs
alpae Nov 4, 2026
880c83d
test(fungi30): run regeneration as the caller and refuse mixed tool v…
alpae Nov 4, 2026
768c468
test(fungi30): quote the container command for paths with spaces
alpae Nov 4, 2026
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57 changes: 57 additions & 0 deletions .github/workflows/python-tests.yml
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name: Python unit tests
# Runs the pytest suite in tests/ against the FastOMA python package.
# Tests marked `slow` only run on the nightly schedule and on manual dispatch.
on:
push:
branches:
- dev
pull_request:
schedule:
- cron: "17 3 * * *"
workflow_dispatch:

concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true

jobs:
pytest:
# pinned: the golden snapshots of tests/test_fungi30.py need the mafft/FastTree versions of this image
runs-on: ubuntu-24.04
name: "pytest | python ${{ matrix.python-version }}"
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.12"]

steps:
- name: Check out code
uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1

- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
with:
python-version: ${{ matrix.python-version }}

# same external tools as the runtime stage of the Dockerfile
- name: Install external tools
run: |
sudo apt-get update
sudo apt-get install -y --no-install-recommends fasttree mafft mmseqs2
mafft --version || true
FastTree -expert 2>&1 | head -1 || true

- name: Install FastOMA
run: |
python -m pip install --upgrade pip
python -m pip install -e . pytest

- name: Run tests
env:
# fail rather than skip the golden snapshots if the tool versions changed
FASTOMA_REQUIRE_GOLDEN: "1"
run: |
if [ "${{ github.event_name }}" = "schedule" ] || [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
python -m pytest -ra
else
python -m pytest -ra -m "not slow"
fi
4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -7,3 +7,7 @@ archive
.gitignore
__pycache__
*.orig

# nf-test working files
.nf-test/
.nf-test.log
3 changes: 3 additions & 0 deletions nf-test.config
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Expand Up @@ -2,6 +2,9 @@ config {
// location for all nf-tests
testsDir "./"

// groovy helper classes available in all tests (e.g. FastomaOutput)
libDir "nf-tests/lib"

// nf-test directory including temporary files for each test
workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"

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61 changes: 20 additions & 41 deletions nf-tests/default.nf.test
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Expand Up @@ -15,62 +15,41 @@ nextflow_pipeline {
}

then {

// Custom function to filter timestamp lines
def filterTimestamps = { file ->
return file.readLines()
.findAll { !it.contains('!date-run') && !it.contains('originVersion') }
}
def out = file(params.output_folder).toPath()

// stable_name: All files + folders in ${params.output_folder}/ with a stable name
def stable_name = getAllFilesFromDir(params.output_folder, relative: true, includeDir: true, ignore: ['stats/*.{html,json,txt}'])
// stable_path: All files in ${params.output_folder}/ with stable content
def stable_path = getAllFilesFromDir(params.output_folder, ignoreFile: 'nf-tests/.nftignore')
def timestamp_files = getAllFilesFromDir(params.output_folder, include:['hogmap/*.hogmap', "FastOMA_HOGs.orthoxml"]).collect { file ->
[name: file.name, md5: listToMD5(filterTimestamps(file))]
}
def csv_files = getAllFilesFromDir(params.output_folder, include:['RootHOGs.tsv', 'OrthologousGroups.tsv', 'orthologs.tsv.gz']).collect { file ->
def csv_data = path(file.path).csv(sep: '\t', header: file.name != 'orthologs.tsv.gz', decompress: file.name.endsWith('.gz'))
def header = csv_data.getColumnNames()
def sorted_rows = csv_data.sort().rows

// Convert back to list of strings
def lines = []
lines.add(header.join('\t')) // Add header line
sorted_rows.each { row ->
lines.add(header.collect { col -> row[col] ?: '' }.join('\t'))
}
return [name: file.name, md5: listToMD5(lines), lineCount: lines.size()]
}
def fixed_line_number_files = getAllFilesFromDir(params.output_folder, include:['RootHOGs.tsv', 'OrthologousGroups.tsv', 'orthologs.tsv.gz', "FastOMA_HOGs.orthoxml", 'hogmap/*.hogmap']).collect { file ->
def line_count
if (file.name.endsWith('.gz')) {
// Use try-with-resources for proper cleanup
new java.util.zip.GZIPInputStream(file.newInputStream()).withCloseable { gzipStream ->
line_count = gzipStream.readLines().size()
}
} else {
line_count = file.readLines().size()
}
return [name: file.name, lineCount: line_count]
// hogmap scores have precision issues across platforms, so only their size is pinned
def hogmap_line_counts = getAllFilesFromDir(params.output_folder, include: ['hogmap/*.hogmap']).collect { f ->
[name: f.name, lineCount: f.readLines().size()]
}

// HOG/OG numbers and row order are not stable, so the inferred orthology is
// compared through order- and id-independent views (nf-tests/lib/FastomaOutput.groovy)
def orthoxml = out.resolve('FastOMA_HOGs.orthoxml')
def geneRefCounts = FastomaOutput.geneRefCounts(orthoxml)

assertAll(
{ assert workflow.success},
{ assert workflow.success },
// every protein is in at most one HOG
{ assert geneRefCounts.findAll { it.value > 1 } == [:] },
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
stable_path,
// List of all files with timestamps filtered out
// does not yet work, as hogmap files have percision issues
// and FastOMA_HOGs is not completely deterministic
// timestamp_files

// files with fixed number of lines
fixed_line_number_files
hogmap_line_counts,
[
orthoxml_elements : FastomaOutput.elementCounts(orthoxml),
hogs : FastomaOutput.canonicalHogs(orthoxml),
roothogs : FastomaOutput.groupPartition(out.resolve('RootHOGs.tsv')),
orthologous_groups: FastomaOutput.groupPartition(out.resolve('OrthologousGroups.tsv')),
ortholog_pairs : FastomaOutput.pairs(out.resolve('orthologs.tsv.gz')),
]
).match() }
)
}
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174 changes: 153 additions & 21 deletions nf-tests/default.nf.test.snap
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Expand Up @@ -48,18 +48,6 @@
"species_tree_checked.nwk:md5,4c82a2f2ffa72a595aaf2fd3deddeff7"
],
[
{
"name": "FastOMA_HOGs.orthoxml",
"lineCount": 194
},
{
"name": "OrthologousGroups.tsv",
"lineCount": 28
},
{
"name": "RootHOGs.tsv",
"lineCount": 28
},
{
"name": "AQUAE.fa.hogmap",
"lineCount": 20
Expand All @@ -71,17 +59,161 @@
{
"name": "MYCGE.fa.hogmap",
"lineCount": 14
},
{
"name": "orthologs.tsv.gz",
"lineCount": 18
}
]
],
{
"orthoxml_elements": {
"orthologGroup": 15,
"paralogGroup": 0,
"gene": 28,
"geneRef": 27
},
"hogs": [
"OG[inter1](sp|O66686|TPIS_AQUAE, sp|O84332|TPIS_CHLTR)",
"OG[inter1](sp|O66778|ENO_AQUAE, sp|O84591|ENO_CHLTR)",
"OG[inter1](sp|O67547|SUCD_AQUAE, tr|O84829|O84829_CHLTR)",
"OG[inter1](sp|O67618|LEPA_AQUAE, sp|O84067|LEPA_CHLTR)",
"OG[inter1](sp|O67736|FOLD_AQUAE, sp|O84081|FOLD_CHLTR)",
"OG[inter1](sp|O67943|CH60_AQUAE, sp|P0C0Z7|CH60_CHLTR)",
"OG[inter2](OG[inter1](sp|O66429|EFTU_AQUAE, sp|P0CD71|EFTU_CHLTR), sp|P13927|EFTU_MYCGE)",
"OG[inter2](OG[inter1](sp|O67032|RF1_AQUAE, sp|O84026|RF1_CHLTR), sp|P47500|RF1_MYCGE)",
"OG[inter2](OG[inter1](sp|O67161|G3P_AQUAE, sp|P0CE13|G3P_CHLTR), sp|P47543|G3P_MYCGE)",
"OG[inter2](sp|O66907|ATPA_AQUAE, sp|P47641|ATPA_MYCGE)",
"OG[inter2](sp|O67828|ATPB_AQUAE, sp|P47639|ATPB_MYCGE)",
"OG[inter2](sp|P17821|DNAK_CHLTR, sp|P47547|DNAK_MYCGE)"
],
"roothogs": [
[
"sp|O66429|EFTU_AQUAE",
"sp|P0CD71|EFTU_CHLTR",
"sp|P13927|EFTU_MYCGE"
],
[
"sp|O66686|TPIS_AQUAE",
"sp|O84332|TPIS_CHLTR"
],
[
"sp|O66778|ENO_AQUAE",
"sp|O84591|ENO_CHLTR"
],
[
"sp|O66907|ATPA_AQUAE",
"sp|P47641|ATPA_MYCGE"
],
[
"sp|O67032|RF1_AQUAE",
"sp|O84026|RF1_CHLTR",
"sp|P47500|RF1_MYCGE"
],
[
"sp|O67161|G3P_AQUAE",
"sp|P0CE13|G3P_CHLTR",
"sp|P47543|G3P_MYCGE"
],
[
"sp|O67547|SUCD_AQUAE",
"tr|O84829|O84829_CHLTR"
],
[
"sp|O67618|LEPA_AQUAE",
"sp|O84067|LEPA_CHLTR"
],
[
"sp|O67736|FOLD_AQUAE",
"sp|O84081|FOLD_CHLTR"
],
[
"sp|O67828|ATPB_AQUAE",
"sp|P47639|ATPB_MYCGE"
],
[
"sp|O67943|CH60_AQUAE",
"sp|P0C0Z7|CH60_CHLTR"
],
[
"sp|P17821|DNAK_CHLTR",
"sp|P47547|DNAK_MYCGE"
]
],
"orthologous_groups": [
[
"sp|O66429|EFTU_AQUAE",
"sp|P0CD71|EFTU_CHLTR",
"sp|P13927|EFTU_MYCGE"
],
[
"sp|O66686|TPIS_AQUAE",
"sp|O84332|TPIS_CHLTR"
],
[
"sp|O66778|ENO_AQUAE",
"sp|O84591|ENO_CHLTR"
],
[
"sp|O66907|ATPA_AQUAE",
"sp|P47641|ATPA_MYCGE"
],
[
"sp|O67032|RF1_AQUAE",
"sp|O84026|RF1_CHLTR",
"sp|P47500|RF1_MYCGE"
],
[
"sp|O67161|G3P_AQUAE",
"sp|P0CE13|G3P_CHLTR",
"sp|P47543|G3P_MYCGE"
],
[
"sp|O67547|SUCD_AQUAE",
"tr|O84829|O84829_CHLTR"
],
[
"sp|O67618|LEPA_AQUAE",
"sp|O84067|LEPA_CHLTR"
],
[
"sp|O67736|FOLD_AQUAE",
"sp|O84081|FOLD_CHLTR"
],
[
"sp|O67828|ATPB_AQUAE",
"sp|P47639|ATPB_MYCGE"
],
[
"sp|O67943|CH60_AQUAE",
"sp|P0C0Z7|CH60_CHLTR"
],
[
"sp|P17821|DNAK_CHLTR",
"sp|P47547|DNAK_MYCGE"
]
],
"ortholog_pairs": [
"sp|O66429|EFTU_AQUAE <-> sp|P0CD71|EFTU_CHLTR",
"sp|O66429|EFTU_AQUAE <-> sp|P13927|EFTU_MYCGE",
"sp|O66686|TPIS_AQUAE <-> sp|O84332|TPIS_CHLTR",
"sp|O66778|ENO_AQUAE <-> sp|O84591|ENO_CHLTR",
"sp|O66907|ATPA_AQUAE <-> sp|P47641|ATPA_MYCGE",
"sp|O67032|RF1_AQUAE <-> sp|O84026|RF1_CHLTR",
"sp|O67032|RF1_AQUAE <-> sp|P47500|RF1_MYCGE",
"sp|O67161|G3P_AQUAE <-> sp|P0CE13|G3P_CHLTR",
"sp|O67161|G3P_AQUAE <-> sp|P47543|G3P_MYCGE",
"sp|O67547|SUCD_AQUAE <-> tr|O84829|O84829_CHLTR",
"sp|O67618|LEPA_AQUAE <-> sp|O84067|LEPA_CHLTR",
"sp|O67736|FOLD_AQUAE <-> sp|O84081|FOLD_CHLTR",
"sp|O67828|ATPB_AQUAE <-> sp|P47639|ATPB_MYCGE",
"sp|O67943|CH60_AQUAE <-> sp|P0C0Z7|CH60_CHLTR",
"sp|O84026|RF1_CHLTR <-> sp|P47500|RF1_MYCGE",
"sp|P0CD71|EFTU_CHLTR <-> sp|P13927|EFTU_MYCGE",
"sp|P0CE13|G3P_CHLTR <-> sp|P47543|G3P_MYCGE",
"sp|P17821|DNAK_CHLTR <-> sp|P47547|DNAK_MYCGE"
]
}
],
"timestamp": "2026-10-20T14:21:18.662761",
"meta": {
"nf-test": "0.9.3",
"nextflow": "26.04.6"
},
"timestamp": "2026-08-25T18:07:32.287389"
"nf-test": "0.9.5",
"nextflow": "24.10.2"
}
}
}
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2 changes: 2 additions & 0 deletions nf-tests/helpers/splice_in/AQUAE.splice
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sp|O66429|EFTU_AQUAE;sp|O67618|LEPA_AQUAE
sp|O66778|ENO_AQUAE
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