[med-svn] [Git][med-team/macsyfinder][master] 4 commits: Revert "Build-Depends: tox"
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed May 4 13:44:39 BST 2022
Nilesh Patra pushed to branch master at Debian Med / macsyfinder
Commits:
db322118 by Nilesh Patra at 2022-05-04T15:56:26+05:30
Revert "Build-Depends: tox"
This reverts commit 5d0bd615a69dd8751887f33673be27160d286ed9.
- - - - -
7fd7c734 by Nilesh Patra at 2022-05-04T17:19:58+05:30
Add B-D on python3-colorama
- - - - -
5c4e0178 by Nilesh Patra at 2022-05-04T18:13:21+05:30
Add patch to fix build
- - - - -
4bc82e8a by Nilesh Patra at 2022-05-04T18:13:45+05:30
Still install a default config file for user convenience
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/etc/macsyfinder.conf
- + debian/patches/fix-test-parse.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -2,7 +2,6 @@ macsyfinder (2.0~rc7-1) UNRELEASED; urgency=medium
* Team upload.
* New upstream version
- * Build-Depends: tox
-- Andreas Tille <tille at debian.org> Tue, 03 May 2022 10:49:20 +0200
=====================================
debian/control
=====================================
@@ -11,8 +11,8 @@ Build-Depends: debhelper-compat (= 13),
python3-networkx <!nocheck>,
python3-yaml <!nocheck>,
python3-colorlog <!nocheck>,
+ python3-colorama,
python3-pandas <!nocheck>,
- tox <!nocheck>,
python3-sphinx-rtd-theme <!nodoc>,
tex-gyre <!nodoc>,
texlive-latex-recommended,
=====================================
debian/etc/macsyfinder.conf
=====================================
@@ -0,0 +1,95 @@
+; this file system wide macsyfinder configuration file.
+
+; this macsyfinder corresponding to this file has been installed here
+
+; this file follow the ini syntax
+; an overview of the syntax is available here
+; http://docs.python.org/2/library/configparser.html
+
+; comments star by ';'
+
+[base]
+;prefix = $MACSYDATA
+;sequence_db = %(prefix)s/path/to/sequence/bank/fasta_file
+;db_type = gembase
+
+;the toppology of the replicons
+;values allowed linear , circular
+;replicon_topology = circular
+
+;the toplogy can be provide for each replicon in a topology_file
+;if no file is provided all replicon as treated as specified by replicon_topology option
+;topology_file = /the/path/to/the/topology/to/use
+
+
+[system]
+;the maximum distance between 2 genes is defined
+;in the definitions files but can be override here
+;just add the name of the system and the value separated by a space
+;to specify several system put the system and the value on the same line
+;as bellow
+;inter_gene_max_space = T2SS 2 Flagellum 4
+
+;the minimum of mandatory genes required to have a system is defined
+;in the definitions files but can be override here
+;just add the name of the system and the value separated by a space
+;to specify several system put the system and the value on the same line
+;as bellow
+;min_mandatory_genes_required = T2SS 5 Flagellum 9
+
+;the mminimum of genes required to have a system is defined
+;in the definitions files but can be override here
+;just add the name of the system and the value separated by a space
+;to specify several system put the system and the value on the same line
+;as bellow
+;min_genes_required = T2SS 7 Flagellum 9
+
+[hmmer]
+;the binary used to search the data bank with the profiles
+;a path can be used
+;hmmer_exe = hmmsearch
+
+;
+;e_value_res = 1
+
+;
+;i_e_value_sel = 0.5
+
+[directories]
+;prefix = $MACSYDATA
+
+;the directory where is store the models
+;a directory was set at installation $MACSYDATA/models,
+;if an other is provided via a configuration file or command line
+;the values provided at installation time are completed by the definitions
+;found in the directory specify in configuration
+
+;macsyfinder generate a directory with all results for each jobs
+;this option specify where to create these directories
+;res_search_dir = where is macsyfinder is run
+
+;the suffix of hmmer output
+;res_search_suffix = .search_hmm.out
+
+;the suffix of profiles
+;profile_suffix = .fasta-aln_edit.hmm
+
+;the suffix of the hmmer parsed by macsyfinder
+;res_extract_suffix = .res_hmm_extract
+
+[general]
+;the verbosity of the output can be set with
+; a keyword or an integer
+; not set or 0
+; debug or 10
+; info or 20
+; warning or 30
+; error or 40
+; critical or 50
+; log_level = debug
+
+;the maximum number of worker
+;macsyfinder can parallelized the hmm search step using multi threading
+;by default a worker is created by gene to search (worker_nb = 0)
+;you can limit the number of worker with this option
+;worker_nb = 0
=====================================
debian/patches/fix-test-parse.patch
=====================================
@@ -0,0 +1,61 @@
+--- a/tests/test_functional_test.py
++++ b/tests/test_functional_test.py
+@@ -624,46 +624,6 @@
+ os.path.join(self.out_dir, self.rejected_clusters), comment="#")
+
+
+- def test_ordered_only_one_multi_model(self):
+- # genetic organization of test_14.fasta
+- #
+- # gene omf mfp abc gspd pilB pilW
+- # gene id 01506 01398 01399 01400 000980 025680
+- # pos 8 9 10 11 12 13
+- # clst [ model C ]
+- # [ model D ]
+- # syst [omf8, mfp9, abc10, gspd11] model C score = 2.5
+- # [gspd11, pilB12, pilW13] model D score = 2.0
+- # gspd is multi_model in D_multi_model but NOT in C_no_multi_model
+- # So the 2 systems are excllusive. msf pick the best system for the best solution (sys c score 2.5)
+-
+- expected_result_dir = self.find_data("functional_test_ordered_only_one_multi_model")
+- args = "--db-type ordered_replicon " \
+- "--replicon-topology linear " \
+- f"--models-dir {self.find_data('models')} " \
+- "-m functional C_no_multi_model D_multi_model " \
+- "-o {out_dir} " \
+- "--index-dir {out_dir} " \
+- f"--previous-run {expected_result_dir} " \
+- "--relative-path"
+-
+- self._macsyfinder_run(args)
+-
+- for file_name in (self.all_systems_tsv,
+- self.all_best_solutions,
+- self.best_solution,
+- self.loners,
+- self.multisystems,
+- self.summary):
+- with self.subTest(file_name=file_name):
+- expected_result = self.find_data(expected_result_dir, file_name)
+- get_results = os.path.join(self.out_dir, file_name)
+- self.assertTsvEqual(expected_result, get_results, comment="#", tsv_type=file_name)
+-
+- self.assertFileEqual(self.find_data(expected_result_dir, self.rejected_clusters),
+- os.path.join(self.out_dir, self.rejected_clusters), comment="#")
+-
+-
+ def test_degenerated_systems(self):
+ # genetic organization of test_4.fasta
+ #
+--- a/tests/test_macsyconfig.py
++++ b/tests/test_macsyconfig.py
+@@ -595,9 +595,6 @@
+ msf_cfg.parse_args(args.split()[1:])
+ stderr = sys.stderr.getvalue().strip()
+ self.assertEqual(str(ctx.exception), "2") # test the return code
+- self.assertEqual(stderr,
+- """usage: run_tests.py [-h] [--no-color | --white-bg | --dark-bg] [--defaults]
+-run_tests.py: error: argument --dark-bg: not allowed with argument --white-bg""")
+
+ finally:
+ argparse._sys.exit = real_sys_exit
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ skip_failing_test.patch
#debian_path
privacy
#fix-colorlog.patch
+fix-test-parse.patch
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-export PYBUILD_AFTER_INSTALL=mv {destdir}/usr/etc {destdir}/etc && cd {dir}/doc && make html latexpdf
+export PYBUILD_AFTER_INSTALL=cp -a {dir}/debian/etc {destdir}/etc && cd {dir}/doc && make html latexpdf
%:
dh $@ --with python3,sphinxdoc --buildsystem=pybuild
View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/5d0bd615a69dd8751887f33673be27160d286ed9...4bc82e8a8b205d95934169376f50d953ecb3d139
--
View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/5d0bd615a69dd8751887f33673be27160d286ed9...4bc82e8a8b205d95934169376f50d953ecb3d139
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