Merge branch 'v2.1.0'

DessimozLab · Nov 25, 2024 · ff5e459 · ff5e459
2 parents 9b0e048 + 15070a9
commit ff5e459
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Showing 15 changed files with 382 additions and 90 deletions.
diff --git a/omamer/HOGParser.py b/omamer/HOGParser.py
@@ -2,6 +2,7 @@
     HOGPROP - Propagation of Gene Ontology (GO) annotations through
     Hierarchical Orthologous Groups (HOGs) from the OMA project.
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2015-2023 Alex Warwick Vesztrocy <[email protected]>
 
     This file is part of HOGPROP. It contains a module for parsing an

diff --git a/omamer/__init__.py b/omamer/__init__.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>
@@ -23,7 +24,7 @@
 from datetime import date
 
 __packagename__ = "omamer"
-__version__ = "2.0.5"
-__copyright__ = "(C) 2019-{:d} Victor Rossier <[email protected]> and Alex Warwick Vesztrocy <[email protected]>".format(
+__version__ = "2.1.0"
+__copyright__ = "(C) 2019-{:d} Victor Rossier <[email protected]> and Alex Warwick Vesztrocy <[email protected]> and Nikolai Romashchenko <[email protected]>".format(
     date.today().year
 )
diff --git a/omamer/_clock.py b/omamer/_clock.py
@@ -0,0 +1,38 @@
+"""
+    OMAmer - tree-driven and alignment-free protein assignment to sub-families
+
+    (C) 2024 Nikolai Romashchenko <[email protected]>
+    (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
+    (C) 2019-2021 Victor Rossier <[email protected]> and
+                  Alex Warwick Vesztrocy <[email protected]>
+
+    This file is part of OMAmer.
+
+    OMAmer is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OMAmer is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+    GNU Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with OMAmer. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import ctypes
+
+# Access the _PyTime_AsSecondsDouble and _PyTime_GetSystemClock functions from pythonapi
+clock = ctypes.pythonapi._PyTime_GetSystemClock
+as_seconds = ctypes.pythonapi._PyTime_AsSecondsDouble
+
+# Set the argument types and return types of the functions
+clock.argtypes = []
+clock.restype = ctypes.c_int64
+
+as_seconds.argtypes = [ctypes.c_int64]
+as_seconds.restype = ctypes.c_double
+
+
diff --git a/omamer/_runners.py b/omamer/_runners.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>

diff --git a/omamer/_utils.py b/omamer/_utils.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>

diff --git a/omamer/database.py b/omamer/database.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>

diff --git a/omamer/hierarchy.py b/omamer/hierarchy.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>

diff --git a/omamer/index.py b/omamer/index.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>

diff --git a/omamer/main.py b/omamer/main.py
@@ -1,6 +1,7 @@
 """
     OMAmer - tree-driven and alignment-free protein assignment to sub-families
 
+    (C) 2024 Nikolai Romashchenko <[email protected]>
     (C) 2022-2023 Alex Warwick Vesztrocy <[email protected]>
     (C) 2019-2021 Victor Rossier <[email protected]> and
                   Alex Warwick Vesztrocy <[email protected]>
@@ -265,6 +266,7 @@ def get_thread_count():
         help="Show metadata about an omamer database.",
         description="Show metadata about an existing omamer database",
     )
+
     info_parser.set_defaults(func=info_db)
     info_parser.add_argument(
         "-d",
@@ -303,4 +305,4 @@ def get_thread_count():
         # call the relevant runner func
         args.func(args)
     else:
-        parser.print_usage()
+        parser.print_usage()