Merge branch 'rel-0.4.0'

Author: alpae

.github/workflows/docker-image.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           submodules: recursive
 
@@ -37,6 +37,9 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
             type=semver,pattern={{major}}
             type=sha
+          labels: |
+            org.opencontainers.image.source=${{ github.repository }}
+            org.opencontainers.image.revision=${{ github.sha }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3

.github/workflows/publish-pypi-release.yml

@@ -10,11 +10,13 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -24,7 +26,4 @@ jobs:
     - name: Build package
       run: hatch build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@15c56dba361d8335944d31a2ecd17d700fc7bcbc
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e

Dockerfile

@@ -1,11 +1,11 @@
-FROM python:3.11-slim as basis
+FROM python:3.11-slim AS basis
 
 # set environment varibles
-ENV PYTHONDONTWRITEBYTECODE 1
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
 
 
-FROM basis as builder
+FROM basis AS builder
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        build-essential \
@@ -29,14 +29,15 @@ RUN ls -la \
     && /app/bin/pip install dist/*.whl
 
 
-FROM basis as runtime
+FROM basis AS runtime
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        fasttree \
        libxml2 \
        mafft \
        mmseqs2 \
        procps \
+       time \
     && apt-get -y autoremove \
     && apt-get -y autoclean \
     && rm -rf /var/lib/apt/lists/*

FastOMA.nf

@@ -237,6 +237,7 @@ process infer_roothogs{
                                --hogmap hogmaps \
                                --splice ${splice_folder} \
                                --out-rhog-folder "omamer_rhogs" \
+                               --min-sequence-length ${params.min_sequence_length} \
                                -vv
     """
 }

FastOMA/__init__.py

@@ -1,3 +1,6 @@
 
 __packagename__ = "FastOMA"
-__version__ = "0.3.5"
+__version__ = "0.4.0"
+
+import logging
+logger = logging.getLogger("FastOMA")

FastOMA/_hog_class.py

@@ -20,8 +20,8 @@
 
 
 import itertools
-from . import _utils_subhog
-from ._wrappers import logger
+from . import _utils_subhog, logger
+
 
 # from .infer_subhogs import conf_infer_subhhogs #fastoma_infer_subhogs #
 
@@ -144,6 +144,9 @@ def taxlevel(self):
     def rhogid(self):
         return self._rhogid
 
+    def __len__(self):
+        return len(self._members)
+
     def get_members(self):
         return set(self._members)
 
@@ -334,10 +337,17 @@ def _sorter_key(sh):
         elif len(element_list) > 1:
             #hog_elemnt = ET.Element('orthologGroup', attrib={"id": str(self._hogid)})
             hog_elemnt = ET.Element('orthologGroup', attrib={"id": str(self._hogid)}, )
-            num_species_tax_hog = len(set([i.split("||")[1] for i in self._members]))  #  'tr|H2MU14|H2MU14_ORYLA||ORYLA||1056022282'
-            completeness_score = round(num_species_tax_hog/self._tax_now.size, 4)
+            species_of_members = set([i.split("||")[1] for i in self._members])  #  'tr|H2MU14|H2MU14_ORYLA||ORYLA||1056022282'
+            num_species_tax_hog = len(species_of_members)
+            mrca = self.taxlevel.get_common_ancestor(
+                *[self.taxlevel.search_nodes(name=x)[0] for x in species_of_members])
+            if mrca != self.taxlevel:
+                logger.info(f"mrca ({mrca.name}) != self.taxlevel ({self.taxlevel.name})")
+                logger.info(f"<{hog_elemnt.tag} {hog_elemnt.attrib}>")
+
+            completeness_score = round(num_species_tax_hog/mrca.size, 4)
             property_element = ET.SubElement(hog_elemnt, "score", attrib={"id": "CompletenessScore", "value": str(completeness_score)})
-            property_element = ET.SubElement(hog_elemnt, "property", attrib={"name": "TaxRange", "value": str(self._tax_now.name)})
+            property_element = ET.SubElement(hog_elemnt, "property", attrib={"name": "TaxRange", "value": str(mrca.name)})
 
             for element in element_list:
                 hog_elemnt.append(element)