Merge branch 'release/0.18.1'

Author: siebrenf

.rtd-environment.yml

@@ -1,7 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   # docs specific packages
   - mock
@@ -13,18 +12,18 @@ dependencies:
   - configparser
   - diskcache
   - feather-format
-  - genomepy >=0.13.0
-  - ipywidgets                    # optional: progress bar in Jupyter notebook
+  - genomepy >=0.14.0
+  # - ipywidgets                    # optional: progress bar in Jupyter notebook
   - iteround
   - jinja2
   - logomaker
   - loguru
   - matplotlib-base >=3.3         # https://matplotlib.org/stable/devel/min_dep_policy.html#list-of-dependency-versions
   - numpy >=1.18                  # https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table
-  - pandas >=1.3.0                # version necessary for ExtraStyler.render()
+  - pandas >=1.3, <3
   - pybedtools >=0.9.0
   - pysam >=0.16
-  - python >=3.6
+  - python >=3.7, <3.12           # Motifsampler & setuptools break from py3.12
   - python-xxhash
   - qnorm  >=0.8.1
   - scikit-learn >=0.23.2         # https://scikit-learn.org/stable/install.html#installing-the-latest-release

.travis.yml

@@ -25,7 +25,7 @@ install:
   - mamba env create -f requirements.yaml
   - source activate gimme
   - python setup.py build  # installs the motif discovery tools
-  - pip install -e .  # installs gimme (in editable mode)
+  - pip install -e . --no-deps --ignore-installed  # installs gimme (in editable mode)
 
 before_script:
   # install Code Climate test coverage reporter

CHANGELOG.md

@@ -5,6 +5,22 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## Unreleased
 
+## [0.18.1] - 2025-10-02
+
+### Changed
+
+- updated dependencies (conda + pypi)
+- updated Maelstrom report (don't show "NO ORTHOLOGS FOUND" if other factors have been found)
+- limit python to 3.11
+  - Motifsampler & setuptools break from 3.12 onwards
+
+### Fixed
+
+- `gimme motifs` uses `--ncpus` where possible (two more places). fixes #265
+- updated pandas code, able to run pandas 2 now! resolves #306
+- updated C code, fixes compiler warnings & error (thanks cameronraysmith!)
+- updated versioneer, able to update configparser now! resolves #315
+
 ## [0.18.0] - 2023-01-11
 
 ### Added

docs/release_checklist.md

@@ -8,8 +8,8 @@ This is mainly for personal use at the moment.
 1. Make sure all tests pass.
 
 ```shell
-mamba env update -f environment.yml
-pytest -vvv
+mamba env update -f requirements.yaml
+pytest -vvv --disable-pytest-warnings
 ```
 
 2. Create release candidate with `git flow`:
@@ -34,7 +34,7 @@ python setup.py sdist
 mamba create -n test python=3.9 pytest
 mamba activate test
 pip install dist/gimmemotifs*.tar.gz
-pytest -vvv
+pytest -vvv --disable-pytest-warnings
 ```
 
 5. Upload to pypi testing server

gimmemotifs/c_metrics.c

@@ -14,12 +14,6 @@
 #include <string.h>
 #include <stdio.h>
 
-#if PY_MAJOR_VERSION >= 3
-    #define PyInt_FromLong PyLong_FromLong
-    #define PyString_Check PyUnicode_Check
-    #define PyString_Size PyUnicode_GET_LENGTH
-#endif
-
 
 void fill_matrix(double matrix[][4], PyObject *matrix_o) {
 	// Parse a PyObject matrix into a C array	
@@ -312,9 +306,7 @@ static PyObject * c_metrics_score(PyObject *self, PyObject * args)
 
 }
 
-int get_truncate_len(len1, len2, pos) {
-	// 
-	
+int get_truncate_len(int len1, int len2, int pos) {
 	if (pos < 0) {
 		len2 += pos;
 	}
@@ -328,7 +320,6 @@ int get_truncate_len(len1, len2, pos) {
 	else {
 		return len1;
 	}
-	
 }
 
 void fill_tmp_matrices(double matrix1[][4], double matrix2[][4], int pos, int l, double tmp_matrix1[][4], double tmp_matrix2[][4]) {
@@ -560,8 +551,6 @@ static PyObject * c_metrics_pwmscan(PyObject *self, PyObject * args)
 
 	if (j_max < 0) { j_max = 0;}
 	int m;
-	int c;
-	double pwm_min = -50;	
 	for (j = 0; j < j_max; j++) {
 		score = 0;
 		rc_score = 0;
@@ -622,9 +611,9 @@ static PyObject * c_metrics_pwmscan(PyObject *self, PyObject * args)
 				PyObject* row = PyList_New(0);
 				x = PyFloat_FromDouble(score);
 				PyList_Append(row, x); Py_DECREF(x);
-				x = PyInt_FromLong((long) j);
+				x = PyLong_FromLong((long) j);
 				PyList_Append(row, x); Py_DECREF(x);
-				x = PyInt_FromLong((long) 1);
+				x = PyLong_FromLong((long) 1);
 				PyList_Append(row, x); Py_DECREF(x);
 				PyList_Append(return_list, row);
 				Py_DECREF(row);
@@ -658,9 +647,9 @@ static PyObject * c_metrics_pwmscan(PyObject *self, PyObject * args)
 					PyObject* row = PyList_New(0);
 					x = PyFloat_FromDouble(score);
 					PyList_Append(row, x); Py_DECREF(x);
-					x = PyInt_FromLong((long) j);
+					x = PyLong_FromLong((long) j);
 					PyList_Append(row, x); Py_DECREF(x);
-					x =  PyInt_FromLong((long) 1);
+					x =  PyLong_FromLong((long) 1);
 					PyList_Append(row, x); Py_DECREF(x);
 					PyList_Append(return_list, row);
 					Py_DECREF(row);
@@ -674,9 +663,9 @@ static PyObject * c_metrics_pwmscan(PyObject *self, PyObject * args)
 			PyObject* row = PyList_New(0);
 			x = PyFloat_FromDouble(maxScores[i]);
 			PyList_Append(row, x);  Py_DECREF(x);
-			x = PyInt_FromLong((long)maxPos[i]);
+			x = PyLong_FromLong((long)maxPos[i]);
 			PyList_Append(row, x); Py_DECREF(x);
-			x = PyInt_FromLong((long)maxStrand[i]);
+			x = PyLong_FromLong((long)maxStrand[i]);
 			PyList_Append(row, x); Py_DECREF(x);
 			PyList_Append(return_list, row);
 			Py_DECREF(row);
@@ -827,9 +816,9 @@ static PyObject * c_metrics_pfmscan(PyObject *self, PyObject * args)
 				PyObject* row = PyList_New(0);
 				x = PyFloat_FromDouble(score);
 				PyList_Append(row, x); Py_DECREF(x);
-				x = PyInt_FromLong((long) j);
+				x = PyLong_FromLong((long) j);
 				PyList_Append(row, x); Py_DECREF(x);
-				x = PyInt_FromLong((long) 1);
+				x = PyLong_FromLong((long) 1);
 				PyList_Append(row, x); Py_DECREF(x);
 				PyList_Append(return_list, row);
 				Py_DECREF(row);
@@ -863,9 +852,9 @@ static PyObject * c_metrics_pfmscan(PyObject *self, PyObject * args)
 					PyObject* row = PyList_New(0);
 					x = PyFloat_FromDouble(score);
 					PyList_Append(row, x); Py_DECREF(x);
-					x = PyInt_FromLong((long) j);
+					x = PyLong_FromLong((long) j);
 					PyList_Append(row, x); Py_DECREF(x);
-					x =  PyInt_FromLong((long) 1);
+					x =  PyLong_FromLong((long) 1);
 					PyList_Append(row, x); Py_DECREF(x);
 					PyList_Append(return_list, row);
 					Py_DECREF(row);
@@ -879,9 +868,9 @@ static PyObject * c_metrics_pfmscan(PyObject *self, PyObject * args)
 			PyObject* row = PyList_New(0);
 			x = PyFloat_FromDouble(maxScores[i]);
 			PyList_Append(row, x);  Py_DECREF(x);
-			x = PyInt_FromLong((long)maxPos[i]);
+			x = PyLong_FromLong((long)maxPos[i]);
 			PyList_Append(row, x); Py_DECREF(x);
-			x = PyInt_FromLong((long)maxStrand[i]);
+			x = PyLong_FromLong((long)maxStrand[i]);
 			PyList_Append(row, x); Py_DECREF(x);
 			PyList_Append(return_list, row);
 			Py_DECREF(row);
@@ -898,43 +887,28 @@ static PyMethodDef CoreMethods[] = {
 	{"c_max_subtotal", c_metrics_max_subtotal, METH_VARARGS,"Test"},
 	{"pfmscan", c_metrics_pfmscan, METH_VARARGS,"Test"},
 	{"pwmscan", c_metrics_pwmscan, METH_VARARGS,"Test"},
-	{NULL, NULL, NULL, 0, NULL}
+	{NULL, NULL, 0, NULL}
 };
 
-#if PY_MAJOR_VERSION >= 3
-    static struct PyModuleDef moduledef = {
-        PyModuleDef_HEAD_INIT,
-        "c_metrics",     /* m_name */
-        "This is a module",  /* m_doc */
-        -1,                  /* m_size */
-        CoreMethods,         /* m_methods */
-        NULL,                /* m_reload */
-        NULL,                /* m_traverse */
-        NULL,                /* m_clear */
-        NULL,                /* m_free */
-    };
-#endif
+static struct PyModuleDef moduledef = {
+    PyModuleDef_HEAD_INIT,
+    "c_metrics",         /* m_name */
+    "This is a module",  /* m_doc */
+    -1,                  /* m_size */
+    CoreMethods,         /* m_methods */
+    NULL,                /* m_reload */
+    NULL,                /* m_traverse */
+    NULL,                /* m_clear */
+    NULL,                /* m_free */
+};
 
 static PyObject * moduleinit(void) {
     PyObject *m;
-#if PY_MAJOR_VERSION >= 3
     m = PyModule_Create(&moduledef);
-#else
-    m = Py_InitModule3("c_metrics", CoreMethods, "c_metrics_module");
-#endif
     return m;
 }
 
 PyMODINIT_FUNC
-#if PY_MAJOR_VERSION >= 3
-    PyInit_c_metrics(void)
-    {
-	return moduleinit();
-    };
-#else
-    initc_metrics(void)
-    {
-	moduleinit();
-    };
-#endif
-
+PyInit_c_metrics(void) {
+    return moduleinit();
+};

gimmemotifs/commands/motifs.py

@@ -170,6 +170,7 @@ def motifs(args):
             genome=args.genome,
             zscore=args.zscore,
             gcnorm=args.gc,
+            ncpus=args.ncpus,
         )
 
     n_input = pd.read_csv(score_table, comment="#", sep="\t").shape[0]
@@ -265,6 +266,7 @@ def motifs(args):
                 zscore=args.zscore,
                 gcnorm=args.gc,
                 bgfile=bgfile,
+                ncpus=args.ncpus,
                 progress=False,
             )
 

gimmemotifs/maelstrom/moap.py

@@ -588,7 +588,7 @@ def fit(self, df_X, df_y):
         self.columns = df_y.columns
         X = df_X.loc[y.index]
 
-        clf = LinearSVR(random_state=self.random_state)
+        clf = LinearSVR(random_state=self.random_state, dual="auto")
         self.model = MultiOutputRegressor(clf, n_jobs=1)
         logger.debug("Fitting model")
         self.model.fit(df_X, df_y)