Skip to content

Commit ff5e459

Browse files
nromashchenkonromashchenko
committed
Merge branch 'v2.1.0'
2 parents 9b0e048 + 15070a9 commit ff5e459

15 files changed

+382
-90
lines changed

‎omamer/HOGParser.py

+1
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
HOGPROP - Propagation of Gene Ontology (GO) annotations through
33
Hierarchical Orthologous Groups (HOGs) from the OMA project.
44
5+
(C) 2024 Nikolai Romashchenko <[email protected]>
56
(C) 2015-2023 Alex Warwick Vesztrocy <[email protected]>
67
78
This file is part of HOGPROP. It contains a module for parsing an

‎omamer/__init__.py

+3-2
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>
@@ -23,7 +24,7 @@
2324
from datetime import date
2425

2526
__packagename__ = "omamer"
26-
__version__ = "2.0.5"
27-
__copyright__ = "(C) 2019-{:d} Victor Rossier <[email protected]> and Alex Warwick Vesztrocy <[email protected]>".format(
27+
__version__ = "2.1.0"
28+
__copyright__ = "(C) 2019-{:d} Victor Rossier <[email protected]> and Alex Warwick Vesztrocy <[email protected]> and Nikolai Romashchenko <[email protected]>".format(
2829
date.today().year
2930
)

‎omamer/_clock.py

+38
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
"""
2+
OMAmer - tree-driven and alignment-free protein assignment to sub-families
3+
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
5+
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
6+
(C) 2019-2021 Victor Rossier <[email protected]> and
7+
Alex Warwick Vesztrocy <[email protected]>
8+
9+
This file is part of OMAmer.
10+
11+
OMAmer is free software: you can redistribute it and/or modify
12+
it under the terms of the GNU Lesser General Public License as published by
13+
the Free Software Foundation, either version 3 of the License, or
14+
(at your option) any later version.
15+
16+
OMAmer is distributed in the hope that it will be useful,
17+
but WITHOUT ANY WARRANTY; without even the implied warranty of
18+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19+
GNU Lesser General Public License for more details.
20+
21+
You should have received a copy of the GNU Lesser General Public License
22+
along with OMAmer. If not, see <http://www.gnu.org/licenses/>.
23+
"""
24+
25+
import ctypes
26+
27+
# Access the _PyTime_AsSecondsDouble and _PyTime_GetSystemClock functions from pythonapi
28+
clock = ctypes.pythonapi._PyTime_GetSystemClock
29+
as_seconds = ctypes.pythonapi._PyTime_AsSecondsDouble
30+
31+
# Set the argument types and return types of the functions
32+
clock.argtypes = []
33+
clock.restype = ctypes.c_int64
34+
35+
as_seconds.argtypes = [ctypes.c_int64]
36+
as_seconds.restype = ctypes.c_double
37+
38+

‎omamer/_runners.py

+1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>

‎omamer/_utils.py

+1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>

‎omamer/database.py

+1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>

‎omamer/hierarchy.py

+1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>

‎omamer/index.py

+1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>

‎omamer/main.py

+3-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
"""
22
OMAmer - tree-driven and alignment-free protein assignment to sub-families
33
4+
(C) 2024 Nikolai Romashchenko <[email protected]>
45
(C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
56
(C) 2019-2021 Victor Rossier <[email protected]> and
67
Alex Warwick Vesztrocy <[email protected]>
@@ -265,6 +266,7 @@ def get_thread_count():
265266
help="Show metadata about an omamer database.",
266267
description="Show metadata about an existing omamer database",
267268
)
269+
268270
info_parser.set_defaults(func=info_db)
269271
info_parser.add_argument(
270272
"-d",
@@ -303,4 +305,4 @@ def get_thread_count():
303305
# call the relevant runner func
304306
args.func(args)
305307
else:
306-
parser.print_usage()
308+
parser.print_usage()

0 commit comments

Comments
 (0)