Merge pull request #16 from JLSteenwyk/accel

Accel

Author: JLSteenwyk

.github/workflows/ci.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -17,30 +17,24 @@ jobs:
         pip install -r requirements.txt
         # make orthosnap CLI available for tests 
         make install
-        # install test dependencies
-        pip install pytest
-        pip install pytest-cov
     - name: Run tests
       run: |
         make test.fast
   test-full:
     runs-on: macos-latest
     env:
-      PYTHON: "3.10"
+      PYTHON: "3.13"
     steps:
     - uses: actions/checkout@master
     - name: Setup Python
       uses: actions/setup-python@master
       with:
-        python-version: "3.10"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
         pip install -r requirements.txt
         # make orthosnap CLI available for tests 
         make install
-        # install test dependencies
-        pip install pytest
-        pip install pytest-cov
     - name: Generate coverage report
       run: |
         make test.coverage

AGENTS.md

@@ -0,0 +1,24 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+Core source lives in `orthosnap/`, with the CLI entry point in `orthosnap/orthosnap.py` and shared utilities split across helper modules (for example `helper.py`, `writer.py`). Tests mirror runtime paths under `tests/` (`unit/` for isolated logic, `integration/` for CLI flows) and reuse fixtures in `tests/samples/`. Documentation is authored with Sphinx in `docs/`; build artifacts land in `docs/_build/` during CI. Reusable data for demonstrations ships in `samples/`.
+
+## Build, Test, and Development Commands
+Create an isolated environment (`python -m venv .venv && source .venv/bin/activate`) before installing. Run `make install` to install the package locally so the `orthosnap` console script is available. Use `make test.fast` for the default CI-equivalent quick check, or `make test.unit` and `make test.integration` when focusing on a specific layer. `make test.coverage` produces `unit.coverage.xml` and `integration.coverage.xml` for upload to Codecov; clean any generated FASTA outputs before committing.
+
+## Coding Style & Naming Conventions
+Target Python 3.9–3.13 and follow PEP 8: four-space indentation, snake_case functions, PascalCase classes, and descriptive module-level constants. Keep functions small, prefer explicit variable names (e.g., `taxa_counts` over `tc`), and include short docstrings for public helpers. Align logging and user-visible messages with existing phrasing in `orthosnap/helper.py`. When adding CLI arguments, route parsing through `parser.py` to remain consistent.
+
+## Testing Guidelines
+Pytest drives all suites. Mark unit-only tests with the default markers and integration cases with `@pytest.mark.integration`. Place new unit tests beside the feature under `tests/unit/` and use fixtures from `tests/samples/` where possible. Run `python -m pytest -k <pattern>` to iterate during development, and ensure `make test` succeeds before opening a pull request. Aim to keep coverage steady; add regression tests for every CLI flag or branch condition.
+
+## Commit & Pull Request Guidelines
+Write concise, present-tense commit messages (e.g., `add delimiter argument`) and group related changes. Reference issues in the body using `Fixes #<id>` when relevant. For pull requests, summarise behaviour changes, call out new dependencies, and attach command outputs or screenshots when UX changes. Confirm CI passes, ensure docs stay accurate (update Sphinx sources when CLI flags change), and request at least one review before merging.
+
+## Environment & Documentation Tips
+Use `requirements.txt` for runtime and packaging deps (supports CPython 3.9 through 3.13) and install doc tooling via `pipenv` inside `docs/` when updating the Sphinx site (`cd docs && pipenv run make html`). Avoid checking in files under `docs/_build/` or temporary trees left by integration tests.
+
+## Performance Improvements In Progress
+- Replace whole-tree `copy.deepcopy` calls in `orthosnap/orthosnap.py` with subtree-level cloning so we only touch the relevant clade per iteration.
+- Precompute a parent lookup for tip nodes to let `get_subtree_tips` reuse cached structure instead of copying the tree for every duplicate gene check.
+- Track `assigned_tips` as a set throughout execution to skip repeated list-to-set conversions while filtering already-handled sequences.

orthosnap/helper.py

@@ -7,7 +7,7 @@
 
 from Bio import Phylo
 from Bio import SeqIO
-from Bio.Phylo.BaseTree import TreeMixin
+from Bio.Phylo.BaseTree import TreeMixin, Tree
 
 
 class InparalogToKeep(Enum):
@@ -40,24 +40,10 @@ def determine_if_dups_are_sister(
     # get first set of subtree tips
     # first_set_of_subtree_tips = subtree_tips[0]
     # first_set_of_subtree_tips = subtree_tips
-    # set if duplicate sequences are sister as True
-    are_sisters = True
-    # create a copy of the tree
-    dup_tree = copy.deepcopy(newtree)
+    ancestor = newtree.common_ancestor(subtree_tips)
+    ancestor_tips = {term.name for term in ancestor.get_terminals()}
 
-    dup_tree = dup_tree.common_ancestor(subtree_tips)
-    _, all_tips = get_all_tips_and_taxa_names(dup_tree, delimiter)
-    if set(all_tips) != set(subtree_tips):
-        are_sisters = False
-
-    # # check if duplicate sequences are sister
-    # for set_of_subtree_tips in subtree_tips[1:]:
-    #     if first_set_of_subtree_tips != set_of_subtree_tips:
-    #         are_sisters = False
-    #     if not are_sisters:
-    #         break
-
-    return are_sisters
+    return ancestor_tips == set(subtree_tips)
 
 
 def get_all_tips_and_taxa_names(tree, delimiter: str):
@@ -83,6 +69,19 @@ def get_all_tips_and_taxa_names(tree, delimiter: str):
     return taxa, all_tips
 
 
+def build_tip_parent_lookup(tree):
+    """Return a mapping from terminal name to its parent clade."""
+
+    tip_parent = dict()
+
+    for parent in tree.find_clades(order="preorder"):
+        for child in parent.clades:
+            if child.is_terminal() and child.name is not None:
+                tip_parent[child.name] = parent
+
+    return tip_parent
+
+
 def check_if_single_copy(taxa: list, all_tips: list):
     """
     check if the input phylogeny is already a single-copy tree
@@ -115,7 +114,7 @@ def get_tips_and_taxa_names_and_taxa_counts_from_subtrees(inter, delimiter: str)
     return taxa_from_terms, terms, counts_of_taxa_from_terms, counts
 
 
-def get_subtree_tips(terms: list, name: str, tree):
+def get_subtree_tips(terms: list, name: str, tip_parent_lookup: dict):
     """
     get lists of subsubtrees from subtree
     """
@@ -124,43 +123,36 @@ def get_subtree_tips(terms: list, name: str, tree):
     subtree_tips = []
     # for individual sequence among duplicate sequences
     for dup in dups:
-        # create a copy of the tree
-        temptree = copy.deepcopy(tree)
-        # get the node path for the duplicate sequence
-        node_path = temptree.get_path(dup)
-        # for the terminals of the parent of the duplicate sequence
-        # get the terminal names and append them to temp
-        temp = []
-        for term in node_path[-2].get_terminals():
-            temp.append(term.name)
+        parent = tip_parent_lookup.get(dup)
+        if parent is None:
+            continue
+        temp = [term.name for term in parent.get_terminals()]
         subtree_tips.append(temp)
 
     return subtree_tips, dups
 
 
 def handle_multi_copy_subtree(
-    all_tips: list,
+    subtree,
     terms: list,
-    newtree,
     subgroup_counter: int,
     fasta: str,
     support: float,
     fasta_dict: dict,
-    assigned_tips: list,
+    assigned_tips: set,
     counts_of_taxa_from_terms,
-    tree,
     snap_trees: bool,
     inparalog_to_keep: InparalogToKeep,
     output_path: str,
     inparalog_handling: dict,
     inparalog_handling_summary: dict,
     delimiter: str,
+    tip_parent_lookup: dict,
 ):
     """
     handling case where subtree contains all single copy genes
     """
-    # prune subtree to get subtree of interest
-    newtree = prune_subtree(all_tips, terms, newtree)
+    newtree = Tree(root=copy.deepcopy(subtree))
 
     # collapse bipartition with low support
     newtree = collapse_low_support_bipartitions(newtree, support)
@@ -171,7 +163,9 @@ def handle_multi_copy_subtree(
         # if the taxon is represented by more than one sequence
         if counts_of_taxa_from_terms[name] > 1:
             # get subtree tips
-            _, dups = get_subtree_tips(terms, name, tree)
+            _, dups = get_subtree_tips(terms, name, tip_parent_lookup)
+            if not dups:
+                continue
 
             # check if subtrees are sister to one another
             # are_sisters = determine_if_dups_are_sister(subtree_tips)
@@ -217,14 +211,13 @@ def handle_multi_copy_subtree(
 
 
 def handle_single_copy_subtree(
-    all_tips: list,
+    subtree,
     terms: list,
-    newtree,
     subgroup_counter: int,
     fasta: str,
     support: float,
     fasta_dict: dict,
-    assigned_tips: list,
+    assigned_tips: set,
     snap_trees: bool,
     output_path: str,
     inparalog_handling: dict,
@@ -233,8 +226,7 @@ def handle_single_copy_subtree(
     """
     handling case where subtree contains all single copy genes
     """
-    # prune subtree to get subtree of interest
-    newtree = prune_subtree(all_tips, terms, newtree)
+    newtree = Tree(root=copy.deepcopy(subtree))
 
     # collapse bipartition with low support
     newtree = collapse_low_support_bipartitions(newtree, support)
@@ -361,7 +353,7 @@ def write_output_fasta_and_account_for_assigned_tips_single_copy_case(
     subgroup_counter: int,
     terms: list,
     fasta_dict: dict,
-    assigned_tips: list,
+    assigned_tips: set,
     snap_tree: bool,
     newtree,
     output_path: str,
@@ -376,7 +368,7 @@ def write_output_fasta_and_account_for_assigned_tips_single_copy_case(
     with open(output_file_name, "w") as output_handle:
         for term in terms:
             SeqIO.write(fasta_dict[term], output_handle, "fasta")
-            assigned_tips.append(term)
+            assigned_tips.add(term)
 
     if snap_tree:
         output_file_name = (

orthosnap/orthosnap.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-import copy
 import os
 import re
 import sys
@@ -11,6 +10,7 @@
 from .args_processing import process_args
 from .helper import (
     check_if_single_copy,
+    build_tip_parent_lookup,
     get_all_tips_and_taxa_names,
     get_tips_and_taxa_names_and_taxa_counts_from_subtrees,
     handle_single_copy_subtree,
@@ -68,6 +68,8 @@ def execute(
     # read input files and midpoint root tree
     tree, fasta_dict = read_input_files(tree, fasta, rooted)
 
+    tip_parent_lookup = build_tip_parent_lookup(tree)
+
     # get list of all tip names and taxa names
     taxa, all_tips = get_all_tips_and_taxa_names(tree, delimiter)
 
@@ -79,7 +81,7 @@ def execute(
     # loop through tree, but skip the root (hence [1:])
     # keep tabs of terms that have already been assigned
     # to a subgroup as well as a counter for that subgroup
-    assigned_tips = []
+    assigned_tips = set()
     subgroup_counter = 0
 
     inparalog_handling = dict()
@@ -95,8 +97,7 @@ def execute(
             inter, delimiter
         )
 
-        # create a copy of the input tree
-        newtree = copy.deepcopy(tree)
+        terms_set = set(terms)
 
         # if a sufficient number of taxa are represented, examine the subtree
         if len(counts_of_taxa_from_terms) >= occupancy:
@@ -105,14 +106,13 @@ def execute(
             # prune tips not part of the subtree of interest
             if (
                 set([1]) == set(counts)
-                and len(list(set(terms) & set(assigned_tips))) == 0
+                and assigned_tips.isdisjoint(terms_set)
             ):
                 subgroup_counter, assigned_tips, \
                     inparalog_handling, inparalog_handling_summary = \
                     handle_single_copy_subtree(
-                        all_tips,
+                        inter,
                         terms,
-                        newtree,
                         subgroup_counter,
                         fasta,
                         support,
@@ -127,26 +127,25 @@ def execute(
             # if any taxon is represented by more than one sequence and
             # the tips have not been assigned to a suborthogroup
             # prune tips not part of the subtree of interest
-            elif len(list(set(terms) & set(assigned_tips))) == 0:
+            elif assigned_tips.isdisjoint(terms_set):
                 subgroup_counter, assigned_tips, \
                     inparalog_handling, inparalog_handling_summary = \
                     handle_multi_copy_subtree(
-                        all_tips,
+                        inter,
                         terms,
-                        newtree,
                         subgroup_counter,
                         fasta,
                         support,
                         fasta_dict,
                         assigned_tips,
                         counts_of_taxa_from_terms,
-                        tree,
                         snap_trees,
                         inparalog_to_keep,
                         output_path,
                         inparalog_handling,
                         inparalog_handling_summary,
                         delimiter,
+                        tip_parent_lookup,
                     )
 
     if report_inparalog_handling:

orthosnap/version.py

@@ -1 +1 @@
-__version__ = "1.3.1"
+__version__ = "1.4.0"

requirements.txt

@@ -1,14 +1,16 @@
-biopython==1.82
-coverage==7.3.2
-Cython==3.0.4
-exceptiongroup==1.1.3
-iniconfig==2.0.0
-mock==5.1.0
-numpy==1.24.0
-packaging==23.2
-pluggy==1.5.0
-pytest==8.1.1
-pytest-cov==4.1.0
-pytest-mock==3.0.0
-tomli==2.0.1
-tqdm==4.66.1
+biopython>=1.85
+coverage>=7.5
+Cython>=3.0.10
+exceptiongroup>=1.2.0
+iniconfig>=2.0.0
+mock>=5.1.0
+numpy>=1.24,<2.1; python_version < "3.10"
+numpy>=2.1; python_version >= "3.10"
+packaging>=23.2
+pluggy>=1.5.0
+pytest>=8.2
+pytest-cov>=5.0
+pytest-mock>=3.12
+tomli>=2.0.1; python_version < "3.11"
+tqdm>=4.66.1
+setuptools>=68

samples/OG0000005.fa.renamed.fa.orthosnap.0.fa

@@ -0,0 +1,30 @@
+>Aspergillus_niger_CBS_513.88|XP_001390755.1
+MSNLRDSETSSQISQTLEADVEKCPGQLPSMGQGKVFPPALPNREDYVVDFDGPDDPEHP
+FNWPLPTKLLISMIACFATFIPSFASGVFAPGSEEAAKAFNVGSEVGILGTTLFVLGFAS
+GPVLWAPASELFGRRWPLTLGLLGGAVFTITSAVSKDIQTLIICRFFAGMFGASPLAVVP
+AVLSDIWNNSHRGAAISVYALFVFVGPLSAPFIGGFITASSLGWRWTLYIPAFVGFAWGA
+ISVFFLRETYASCLLLSKAVTLRRLTGNWGVHAKQEEVEVDIQQLIQKYFTRPLRMLVTE
+PIILVISLYMSFIYGIVYALLEAYPYVFESVYGMSMGIDGLPFIGIIIGQLAACGFILSQ
+QSAYVKKLAANNNVPIPEWRLETVVIGAPVFTAGIFWFSWTGFTASIHWMAPTAAGVLIG
+FGILCIFLPCFNYLVDSFLPVAASTVAANIILRSSVAAGFPLFSKQMFANLGVQWAGTLL
+GCLSAIMIPIPFLFRAYGPRLRGEGRQNSR
+>Aspergillus_awamori_IFM_58123|GCB21319.1
+MSNLRDSETSSQISQTLEADVEKCPGQLPSMGQGKVFPPALPNREDYVVDFDGPDDPEHP
+FNWPLSTKLLISTIACFATFIPSFASGIFAPGAEEAAKAFNVGSEVGILGTTLFVLGFAS
+GPVLWAPASELFGRRWPLTLGLLGGAVFTIASAVSKDIQTLIICRFFAGMFGASPLAVVP
+AVLSDIWNNSHRGAAISVYALFVFVGPLSAPFIGGFITASSLGWRWTLYIPAFVGFAWGA
+ISVFFLRETYASCLLLSKAATLRRLTGNWGVHAKQEEVEVDIQQLIQKYFTRPLRMLVTE
+PIILVISLYMSFIYGIVYALLEAYPYVFESVYGMSMGINSLPFIGIIIGQLAACGFILSQ
+QSAYVKKLVANNNVPIPEWRLEIVVIGAPVFTAGIFWFSWTGFTASIHWMAPTAAGVLIG
+AASTVAANIILRSSVAAGFPLFSKQMFANLGVQWAGTLLGCLSAIMIPIPFLFRAYGPRL
+RGEGRQNSR
+>Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05698-RA
+MESPKLYESSTPLSQMSNSKENIRPFNPAQEITDSLQHQLVVGSSHGSTKKDNRPLTIGA
+GKSFPPPLVDPDNYVVEFDGPDDPEHPYNWSYFLKLRISAIACLGTLTASFTSAIFAPGA
+SHASKAFGVGLEVGTLGTTLYILGFASGPLIWAPTSELIGRRWPLTIGMLGVAIFTISAA
+VCKDIQTLIICRFFAGLFGASQLSVVPAVLSDVYNSSQRGTAITIYSLTVFGGPFSAPFI
+GGFISSSSLGWRWTLYISAFMGFASVSLFILLLKETYAPLLLVAKAAAIRQQTFNWGIHA
+KLDEVKVDVHELFHKYFTRPLKILITEPIVLLISLYMSFIYGLVYALLEAYPYVFESVYG
+MSPGVGGLPFIALIIGQLLACGFIITQNSSYAKKLAANGNVAVPEWRLSPAIVGAPVFTV
+GIFWFGWTSFTSRLHWMAPTAAGVLIGFGVLCIFLPCFNYLVDSYLPLAASTVAANIILR
+SAVAAGFPLFSKQMFERLGVQWAATLLGCLAATMIPIPLVFRAFGPLLRGKSRSAP