Installation
MacSyFinder works with models for macromolecular systems that are not shipped with it, you have to install them separately. See the macsydata section below. We also provide container so you can use macsyfinder directly.
MacSyFinder dependencies
Python version >=3.10 is required to run MacSyFinder: https://docs.python.org/3.10/index.html
MacSyFinder has one program dependency:
the Hmmer program, version 3.1 or greater (http://hmmer.org/).
The hmmsearch program should be installed (e.g., in the PATH) in order to use MacSyFinder. Otherwise, the paths to this executable must be specified in the command-line: see the command-line options.
MacSyFinder also relies on some Python library dependencies:
colorlog
colorama
pyyaml
packaging
networkx
pandas
GitPython
sphinx
sphinx_rtd_theme
sphinx-autodoc-typehints
sphinxcontrib-svg2pdfconverter
coverage
build
ruff
pre-commit
These dependencies will be automatically retrieved and installed when using pip for installation (see below).
MacSyFinder Installation and testing procedures
Installation steps:
Make sure every required dependency/software is present.
By default MacSyFinder will try to use hmmsearch in your PATH. If hmmsearch is not in the PATH, you have to set the absolute path to hmmsearch in a configuration file or in the command-line upon execution. If the tools are not in the path, some test will be skipped and a warning will be raised.
installation in a virtualenv
# create a new virtaulenv
python3 -m venv macsyfinder
# activate it
cd macsyfinder
source bin/activate
# clone/install the project in editable mode
git clone
cd macsyfinder
python3 -m pip install -e .[dev]
# install tools to ensure coding style
pre-commit install
To exit the virtualenv just execute the deactivate command.
source macsyfinder/bin/activate
Then run macsyfinder or macsydata.
Note
from 2.1.4 version, MacSyFinder has adopted ruff as linter and pre-commit to ensure the coding style. please read CONTRIBUTING.md guide lines.
Testing
MacSyFinder project use unittest framework (included in the standard library) to test the code.
All tests stuff is in tests directory.
The data directory contains data needed by the tests
in the __init__.py file a MacsyTest class is defined and should be the base of all testcase use in the project
each test_*.py represent a file containing unit or functional tests
To run all the tests (in the virtualenv)
python -m unittest discover
To increase verbosity of output
python -m unittest discover -vv
...
test_average_wholeness (tests.test_solution.SolutionTest.test_average_wholeness) ... ok
test_gt (tests.test_solution.SolutionTest.test_gt) ... ok
test_hits_number (tests.test_solution.SolutionTest.test_hits_number) ... ok
test_hits_positions (tests.test_solution.SolutionTest.test_hits_positions) ... ok
test_iteration (tests.test_solution.SolutionTest.test_iteration) ... ok
test_lt (tests.test_solution.SolutionTest.test_lt) ... ok
test_score (tests.test_solution.SolutionTest.test_score) ... ok
test_sorting (tests.test_solution.SolutionTest.test_sorting) ... ok
test_systems (tests.test_solution.SolutionTest.test_systems) ... ok
test_get_def_to_detect (tests.test_utils.TestUtils.test_get_def_to_detect) ... ok
test_get_replicon_names_bad_type (tests.test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok
test_get_replicon_names_gembase (tests.test_utils.TestUtils.test_get_replicon_names_gembase) ... ok
test_get_replicon_names_ordered (tests.test_utils.TestUtils.test_get_replicon_names_ordered) ... ok
test_get_replicon_names_unordered (tests.test_utils.TestUtils.test_get_replicon_names_unordered) ... ok
test_parse_time (tests.test_utils.TestUtils.test_parse_time) ... ok
test_threads_available (tests.test_utils.TestUtils.test_threads_available) ... ok
----------------------------------------------------------------------
Ran 548 tests in 34.265s
OK
The tests must be in python file (.py) starting with with test_ It’s possible to specify one or several test files, one module, or one class in a module or a method in a Test class.
Test the test_package module
python -m unittest -vv tests.test_package
test_init (tests.test_package.TestLocalModelIndex.test_init) ... ok
test_repos_url (tests.test_package.TestLocalModelIndex.test_repos_url) ... ok
test_check (tests.test_package.TestPackage.test_check) ... ok
test_check_bad_metadata (tests.test_package.TestPackage.test_check_bad_metadata) ... ok
test_check_dir_in_profile (tests.test_package.TestPackage.test_check_dir_in_profile) ... ok
...
test_list_package_vers (tests.test_package.TestRemoteModelIndex.test_list_package_vers) ... ok
test_list_packages (tests.test_package.TestRemoteModelIndex.test_list_packages) ... ok
test_remote_exists (tests.test_package.TestRemoteModelIndex.test_remote_exists) ... ok
test_repos_url (tests.test_package.TestRemoteModelIndex.test_repos_url) ... ok
test_unarchive (tests.test_package.TestRemoteModelIndex.test_unarchive) ... ok
test_url_json (tests.test_package.TestRemoteModelIndex.test_url_json) ... ok
test_url_json_reach_limit (tests.test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok
----------------------------------------------------------------------
Ran 56 tests in 0.242s
OK
Test only the class TestPackage (this module contains 3 classes)
python -m unittest -vv tests.test_package.TestPackage
test_check (tests.test_package.TestPackage.test_check) ... ok
test_check_bad_metadata (tests.test_package.TestPackage.test_check_bad_metadata) ... ok
test_check_dir_in_profile (tests.test_package.TestPackage.test_check_dir_in_profile) ... ok
test_check_empty_profile (tests.test_package.TestPackage.test_check_empty_profile) ... ok
test_check_metadata (tests.test_package.TestPackage.test_check_metadata) ... ok
test_check_metadata_no_cite (tests.test_package.TestPackage.test_check_metadata_no_cite) ... ok
...
test_metadata (tests.test_package.TestPackage.test_metadata) ... ok
test_profile_with_bad_ext (tests.test_package.TestPackage.test_profile_with_bad_ext) ... ok
----------------------------------------------------------------------
Ran 42 tests in 0.151s
OK
Test only the method test_metadata from the test Class TestPackage in module test_package
python -m unittest -vv tests.test_package.TestPackage.test_metadata
test_metadata (tests.test_package.TestPackage.test_metadata) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.005s
OK
Coverage
To compute the tests coverage, we use the coverage package. The package is automatically installed if you have installed macsyfinder with the dev target see installation The coverage package is setup in the pyproject.toml configuration file
To compute the coverage
coverage run
...
test_lt (tests.test_solution.SolutionTest.test_lt) ... ok
test_score (tests.test_solution.SolutionTest.test_score) ... ok
test_sorting (tests.test_solution.SolutionTest.test_sorting) ... ok
test_systems (tests.test_solution.SolutionTest.test_systems) ... ok
test_get_def_to_detect (tests.test_utils.TestUtils.test_get_def_to_detect) ... ok
test_get_replicon_names_bad_type (tests.test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok
test_get_replicon_names_gembase (tests.test_utils.TestUtils.test_get_replicon_names_gembase) ... ok
test_get_replicon_names_ordered (tests.test_utils.TestUtils.test_get_replicon_names_ordered) ... ok
test_get_replicon_names_unordered (tests.test_utils.TestUtils.test_get_replicon_names_unordered) ... ok
test_parse_time (tests.test_utils.TestUtils.test_parse_time) ... ok
test_threads_available (tests.test_utils.TestUtils.test_threads_available) ... ok
----------------------------------------------------------------------
Ran 548 tests in 34.485s
OK
Then display a report
coverage report
Name Stmts Miss Branch BrPart Cover
--------------------------------------------------------------------------
macsypy/__init__.py 57 4 12 1 93%
macsypy/cluster.py 218 1 122 2 99%
macsypy/config.py 390 10 160 9 97%
macsypy/database.py 204 3 74 1 99%
macsypy/definition_parser.py 220 3 76 2 98%
macsypy/error.py 9 0 0 0 100%
macsypy/gene.py 143 4 48 3 96%
macsypy/hit.py 199 1 83 2 99%
macsypy/licenses.py 14 1 2 1 88%
macsypy/metadata.py 126 0 76 2 99%
macsypy/model.py 127 0 58 0 100%
macsypy/model_conf_parser.py 62 0 16 0 100%
macsypy/package.py 326 9 144 5 96%
macsypy/profile.py 116 7 34 1 95%
macsypy/registries.py 189 5 80 6 96%
macsypy/report.py 122 0 44 2 99%
macsypy/scripts/__init__.py 0 0 0 0 100%
macsypy/scripts/macsy_gembase_split.py 94 2 30 3 96%
macsypy/scripts/macsy_merge_results.py 201 15 102 8 91%
macsypy/scripts/macsyconfig.py 242 3 108 4 98%
macsypy/scripts/macsydata.py 690 62 209 16 90%
macsypy/scripts/macsyfinder.py 551 23 243 10 96%
macsypy/scripts/macsyprofile.py 247 5 86 6 97%
macsypy/search_genes.py 80 7 24 3 90%
macsypy/serialization.py 133 4 72 3 97%
macsypy/solution.py 97 0 74 0 100%
macsypy/system.py 397 3 204 0 99%
macsypy/utils.py 69 0 33 1 99%
--------------------------------------------------------------------------
TOTAL 5323 172 2214 91 96%
or generate a html report
coverage html
Wrote HTML report to htmlcov/index.html
The results are in the htmlcov directory. With you favourite web browser, open the index.html file. for more options please refer to the coverage documentation .
