ci(semantic-release): Add semantic release.

[skip ci]
Ecogenomics · Dec 12, 2023 · 9717f45 · 9717f45
1 parent 7b2417c
commit 9717f45
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diff --git a/.github/workflows/build-publish.yml b/.github/workflows/build-publish.yml
@@ -15,7 +15,7 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           cache: npm
-          node-version: lts
+          node-version: lts/Hydrogen
       - run: npm install
       - run: npx semantic-release --dry-run
         id: semantic_release
@@ -25,7 +25,7 @@ jobs:
         with:
           name: semantic-release
           path: |
-            betula/__init__.py
+            gtdb_precurate/__init__.py
             CHANGELOG.md
           retention-days: 1
     outputs:
@@ -72,7 +72,7 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           cache: npm
-          node-version: lts
+          node-version: lts/Hydrogen
       - run: npm install
       - run: npx semantic-release
         env:

diff --git a/.releaserc b/.releaserc
@@ -9,7 +9,7 @@
     [
       "@semantic-release/exec",
       {
-        "verifyReleaseCmd": "sed -i \"s/.*__version__.*/__version__ = '${nextRelease.version}'/g\" betula/__init__.py && echo version=${nextRelease.version} >> $GITHUB_OUTPUT"
+        "verifyReleaseCmd": "sed -i \"s/.*__version__.*/__version__ = '${nextRelease.version}'/g\" gtdb_precurate/__init__.py && echo version=${nextRelease.version} >> $GITHUB_OUTPUT"
       }
     ],
     [
@@ -23,7 +23,7 @@
       {
         "assets": [
           "CHANGELOG.md",
-          "betula/__init__.py"
+          "gtdb_precurate/__init__.py"
         ],
         "message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"
       }

diff --git a/README.md b/README.md
@@ -1,2 +1,30 @@
-# betula
-Automatic pre-curation of GTDB trees.
+# GTDB Precurate
+
+[![PyPI](https://img.shields.io/pypi/v/gtdb_precurate.svg)](https://pypi.python.org/pypi/gtdb_precurate)
+
+`gtdb_precurate` is an internally used tool used that provides automatic pre-curation of GTDB trees.
+
+## Installation
+
+gtdb_precurate is available on PyPI and can be installed with pip:
+
+```bash
+pip install gtdb_precurate
+```
+
+## Usage
+
+After a successful install, the `gtdb_precurate` command should be available.
+
+The following positional arguments are required:
+
+* `metadata` - This is the path to the metadata file, it should contain a header as the first line.
+    The only requirement is that it has the following columns: `formatted_accession` and `ncbi_wgs_formatted`.
+* `red_dict` - This is the path to the RED dictionary output by PhyloRank.
+* `red_decorated_tree` - This is the path to the scaled RED decorated output by PhyloRank.
+* `out_directory` - This is the path to the directory where the output files will be written.
+
+The following optional arguments are available:
+
+* `--min-bootstrap` - This is the minimum bootstrap value to consider a node to be supported. Default: 95.0.
+* `--debug` - This enables debug logging. Default: False.
diff --git a/betula/__init__.py b/betula/__init__.py
diff --git a/gtdb_precurate/__init__.py b/gtdb_precurate/__init__.py
@@ -0,0 +1,15 @@
+__author__ = 'Aaron Mussig'
+__author_email__ = '[email protected]'
+__copyright__ = 'Copyright 2023'
+__credits__ = ['Aaron Mussig']
+__description__ = 'Automatic pre-curation of GTDB trees.'
+__email__ = '[email protected]'
+__license__ = 'GPL3'
+__maintainer__ = 'Aaron Mussig'
+__maintainer_email__ = '[email protected]'
+__name__ = 'gtdb_precurate'
+__python_requires__ = '>=3.8'
+__status__ = 'Production'
+__title__ = 'GTDB Precurate'
+__url__ = 'https://github.com/Ecogenomics/gtdb_precurate'
+__version__ = '1.0.0'
diff --git a/betula/__main__.py → gtdb_precurate/__main__.py b/betula/__main__.py → gtdb_precurate/__main__.py
@@ -3,13 +3,13 @@
 
 import typer
 
-from betula import __version__
-from betula.method.create_denovo import create_denovo_clusters
-from betula.model.metadata import MetadataFile
-from betula.model.ranks import RANKS
-from betula.model.red_dict import RedDict
-from betula.model.tree import Tree
-from betula.util.logger import init_logger
+from gtdb_precurate import __version__
+from gtdb_precurate.method.create_denovo import create_denovo_clusters
+from gtdb_precurate.model.metadata import MetadataFile
+from gtdb_precurate.model.ranks import RANKS
+from gtdb_precurate.model.red_dict import RedDict
+from gtdb_precurate.model.tree import Tree
+from gtdb_precurate.util.logger import init_logger
 
 
 def main(
@@ -25,14 +25,14 @@ def main(
 
     # Initialise the logger
     log = init_logger(out_directory, debug)
-    log.info(f'betula v{__version__}')
-    log.info(f'betula {" ".join(sys.argv[1:])}')
+    log.info(f'gtdb_precurate v{__version__}')
+    log.info(f'gtdb_precurate {" ".join(sys.argv[1:])}')
 
     # Create the output paths
     if 'red_decorated' in red_decorated_tree.name:
-        tree_path_out = out_directory / red_decorated_tree.name.replace('red_decorated', 'betula')
+        tree_path_out = out_directory / red_decorated_tree.name.replace('red_decorated', 'gtdb_precurate')
     else:
-        tree_path_out = out_directory / f'{red_decorated_tree.stem}.betula{red_decorated_tree.suffix}'
+        tree_path_out = out_directory / f'{red_decorated_tree.stem}.gtdb_precurate{red_decorated_tree.suffix}'
     report_path_out = out_directory / f'{tree_path_out.stem}_report.tsv'
 
     # Read the RED dictionary

diff --git a/betula/method/__init__.py → gtdb_precurate/method/__init__.py b/betula/method/__init__.py → gtdb_precurate/method/__init__.py
diff --git a/betula/method/create_denovo.py → gtdb_precurate/method/create_denovo.py b/betula/method/create_denovo.py → gtdb_precurate/method/create_denovo.py
@@ -1,11 +1,11 @@
 import logging
 from collections import defaultdict
 
-from betula.model.metadata import MetadataFile
-from betula.model.node_label import NodeLabel
-from betula.model.ranks import RANKS
-from betula.model.red_dict import RedDict
-from betula.model.tree import Tree
+from gtdb_precurate.model.metadata import MetadataFile
+from gtdb_precurate.model.node_label import NodeLabel
+from gtdb_precurate.model.ranks import RANKS
+from gtdb_precurate.model.red_dict import RedDict
+from gtdb_precurate.model.tree import Tree
 
 
 def get_gids_missing_ranks(tree):
@@ -106,7 +106,7 @@ def create_taxon(rank, meta, new_taxa, tree, gids):
 def create_ranks(d_rank_to_leaf_candidates, tree, meta):
     # We will now iterate from the highest to lower rank to find shared nodes
     created = set()
-    log = logging.getLogger('betula')
+    log = logging.getLogger('gtdb_precurate')
     for cur_rank, d_leaf_to_candidate_node in sorted(d_rank_to_leaf_candidates.items(),
                                                      key=lambda x: RANKS.index(x[0])):
 
@@ -142,7 +142,7 @@ def create_denovo_clusters(
 ):
     """Creates de novo clusters from the specified tree and metadata."""
 
-    log = logging.getLogger('betula')
+    log = logging.getLogger('gtdb_precurate')
 
     # First, we need to find all genomes that are missing ranks
     d_leaf_to_missing_ranks = get_gids_missing_ranks(tree)

diff --git a/betula/model/__init__.py → gtdb_precurate/model/__init__.py b/betula/model/__init__.py → gtdb_precurate/model/__init__.py
diff --git a/betula/model/metadata.py → gtdb_precurate/model/metadata.py b/betula/model/metadata.py → gtdb_precurate/model/metadata.py
diff --git a/betula/model/node_label.py → gtdb_precurate/model/node_label.py b/betula/model/node_label.py → gtdb_precurate/model/node_label.py
diff --git a/betula/model/ranks.py → gtdb_precurate/model/ranks.py b/betula/model/ranks.py → gtdb_precurate/model/ranks.py
diff --git a/betula/model/red_dict.py → gtdb_precurate/model/red_dict.py b/betula/model/red_dict.py → gtdb_precurate/model/red_dict.py
@@ -1,7 +1,7 @@
 import json
 from pathlib import Path
 
-from betula.model.ranks import RANKS
+from gtdb_precurate.model.ranks import RANKS
 
 
 class RedDict:

diff --git a/betula/model/tree.py → gtdb_precurate/model/tree.py b/betula/model/tree.py → gtdb_precurate/model/tree.py
@@ -4,9 +4,9 @@
 
 import dendropy
 
-from betula.model.node_label import NodeLabel
-from betula.model.ranks import RANKS, TaxString
-from betula.util.tree import parse_node_label
+from gtdb_precurate.model.node_label import NodeLabel
+from gtdb_precurate.model.ranks import RANKS, TaxString
+from gtdb_precurate.util.tree import parse_node_label
 
 
 class Tree:

diff --git a/betula/util/__init__.py → gtdb_precurate/util/__init__.py b/betula/util/__init__.py → gtdb_precurate/util/__init__.py
diff --git a/betula/util/logger.py → gtdb_precurate/util/logger.py b/betula/util/logger.py → gtdb_precurate/util/logger.py
@@ -5,7 +5,7 @@
 
 def init_logger(out_dir: Path, debug=False):
     # Logger setup
-    logger = logging.getLogger('betula')
+    logger = logging.getLogger('gtdb_precurate')
     if debug:
         logger.setLevel(logging.DEBUG)
     else:
@@ -20,7 +20,7 @@ def init_logger(out_dir: Path, debug=False):
     logger.addHandler(console_handler)
 
     # File handler
-    file_handler = logging.FileHandler(out_dir / 'betula.log')
+    file_handler = logging.FileHandler(out_dir / 'gtdb_precurate.log')
     file_handler.setFormatter(formatter)
     logger.addHandler(file_handler)
 

diff --git a/betula/util/tree.py → gtdb_precurate/util/tree.py b/betula/util/tree.py → gtdb_precurate/util/tree.py
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,5 +1,5 @@
 {
-  "name": "betula",
+  "name": "gtdb_precurate",
   "devDependencies": {
     "@semantic-release/github": "^9.2.5",
     "@semantic-release/changelog": "^6.0.3",

diff --git a/setup.py b/setup.py
@@ -0,0 +1,60 @@
+import os
+import re
+
+from setuptools import setup, find_packages
+
+
+def read_meta():
+    """Read each of the keys stored in __init__.py
+
+    Returns
+    -------
+    dict[str, str]
+        A dictionary containing each of the string key value pairs.
+    """
+    path = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'gtdb_precurate/__init__.py')
+    with open(path) as fh:
+        hits = re.findall(r'__(\w+)__ ?= ?["\'](.+)["\']\n', fh.read())
+    return {k: v for k, v in hits}
+
+
+def readme():
+    with open('README.md') as f:
+        return f.read()
+
+
+meta = read_meta()
+setup(
+    author=meta['author'],
+    author_email=meta['author_email'],
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+        'Natural Language :: English',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+    ],
+    data_files=[("", ["LICENSE"])],
+    description=meta['description'],
+    entry_points={
+        'console_scripts': [
+            'gtdb_precurate = gtdb_precurate.__main__:main'
+        ]
+    },
+    install_requires=["dendropy>=4.1.0"],
+    license=meta['license'],
+    long_description=readme(),
+    long_description_content_type='text/markdown',
+    maintainer=meta['maintainer'],
+    maintainer_email=meta['maintainer_email'],
+    name=meta['name'],
+    packages=find_packages(),
+    python_requires=meta['python_requires'],
+    url=meta['url'],
+    version=meta['version']
+)