Installation
MacSyFinder works with models for macromolecular systems that are not shipped with it, you have to install them separately. See the msf_data 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:
MacSyLib
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 msf_data.
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_check_choice (tests.test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok
test_check_dir (tests.test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok
test_check_exe (tests.test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok
test_check_file (tests.test_macsyconfig.TestMacsyconfig.test_check_file) ... ok
test_check_float (tests.test_macsyconfig.TestMacsyconfig.test_check_float) ... ok
test_check_positive_int (tests.test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok
test_check_str (tests.test_macsyconfig.TestMacsyconfig.test_check_str) ... ok
test_functional_dark_theme (tests.test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok
test_functional_file_already_exists (tests.test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok
test_parse_args (tests.test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok
test_set_base_options (tests.test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok
test_set_general_options (tests.test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok
test_set_hmmer_options (tests.test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok
test_set_path_options (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok
test_set_path_options_with_system_models_dir (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok
test_set_score_options (tests.test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok
test_set_section (tests.test_macsyconfig.TestMacsyconfig.test_set_section) ... ok
test_set_section_use_defaults (tests.test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok
test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok
test_get_version_message (tests.test_macsyfinder.TestMacsyfinder.test_get_version_message) ... ok
test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok
test_list_models_no_permissions (tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions) ... ok
test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok
test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok
test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok
test_cmde (tests.test_scripts.Test_macsyfinder.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_config.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_data.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_merge.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_profile.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_split.test_cmde) ... ok
----------------------------------------------------------------------
Ran 85 tests in 8.339s
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_macsyfinder module
python -m unittest -vv tests.test_macsyfinder
test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok
test_get_version_message (tests.test_macsyfinder.TestMacsyfinder.test_get_version_message) ... ok
test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok
test_list_models_no_permissions (tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions) ... ok
test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok
test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok
test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok
----------------------------------------------------------------------
Ran 7 tests in 1.773s
OK
Test only the class TestMacsyfinder
python -m unittest -vv tests.test_macsyfinder.TestMacsyfinder
test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok
test_get_version_message (tests.test_macsyfinder.TestMacsyfinder.test_get_version_message) ... ok
test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok
test_list_models_no_permissions (tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions) ... ok
test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok
test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok
test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok
----------------------------------------------------------------------
Ran 7 tests in 1.862s
OK
Test only the method test_list_models_no_permissions from the test Class TestMacsyfinder in module test_macsyfinder
python -m unittest -vv tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions
test_list_models_no_permissions (tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.000s
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_set_score_options (tests.test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok
test_set_section (tests.test_macsyconfig.TestMacsyconfig.test_set_section) ... ok
test_set_section_use_defaults (tests.test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok
test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok
test_get_version_message (tests.test_macsyfinder.TestMacsyfinder.test_get_version_message) ... ok
test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok
test_list_models_no_permissions (tests.test_macsyfinder.TestMacsyfinder.test_list_models_no_permissions) ... ok
test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok
test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok
test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok
test_cmde (tests.test_scripts.Test_macsyfinder.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_config.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_data.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_merge.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_profile.test_cmde) ... ok
test_cmde (tests.test_scripts.Test_msf_split.test_cmde) ... ok
----------------------------------------------------------------------
Ran 85 tests in 8.339s
OK
Then display a report
coverage report
Name Stmts Miss Branch BrPart Cover
----------------------------------------------------------------------------------
src/macsyfinder/__init__.py 23 2 0 0 91%
src/macsyfinder/io.py 11 0 4 0 100%
src/macsyfinder/scripts/macsy_gembase_split.py 95 2 22 3 96%
src/macsyfinder/scripts/macsy_merge_results.py 203 15 72 8 90%
src/macsyfinder/scripts/macsyconfig.py 245 5 88 4 97%
src/macsyfinder/scripts/msf.py 237 8 48 4 96%
----------------------------------------------------------------------------------
TOTAL
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 .