Fixed shiftetd correlation for 1 node

mdevaluate/correlation.py

@@ -156,16 +156,21 @@ def shifted_correlation(function, frames, selector=None, segments=10,
     idx = np.unique(np.int_(ls) - 1)
     t = np.array([frames[i].time for i in idx]) - frames[0].time
     
-    pool = ProcessPool(nodes=nodes)
+    if nodes==1:
-    try:
+        result = np.array([get_correlation(start_frame, idx=idx, 
-        result = np.array(pool.map(partial(get_correlation, idx=idx, 
+                                            selector=selector)
-                                           selector=selector), 
+                            for start_frame in start_frames])
-                                   start_frames))
+    else:
-    except Exception:
+        pool = ProcessPool(nodes=nodes)
-        logger.warning("Something went wrong while calculating the shifted correlation!")
+        try:
-    finally:
+            result = np.array(pool.map(partial(get_correlation, idx=idx, 
-        pool.terminate()
+                                               selector=selector), 
-        pool.restart()                           
+                                       start_frames))
+        except Exception:
+            logger.warning("Something went wrong while calculating the shifted correlation!")
+        finally:
+            pool.terminate()
+            pool.restart()                           
     
     if average == True:
         clean_result = []

requirements.txt

@@ -1,44 +1,65 @@
+alabaster==0.7.12
 anyio==3.6.2
 argon2-cffi==21.3.0
 argon2-cffi-bindings==21.2.0
-asttokens==2.1.0
+arrow==1.2.3
+astroid==2.12.12
+atomicwrites==1.4.1
 attrs==22.1.0
+autopep8==1.6.0
+Babel==2.11.0
 backcall==0.2.0
 beautifulsoup4==4.11.1
+binaryornot==0.4.4
 biopython==1.79
+black==22.10.0
 bleach==5.0.1
 certifi==2022.9.24
 cffi==1.15.1
+chardet==5.0.0
 charset-normalizer==2.1.1
 click==8.1.3
 cloudpickle==2.2.0
 contourpy==1.0.6
+cookiecutter==2.1.1
+cryptography==38.0.3
 cycler==0.11.0
 dask==2022.10.2
 debugpy==1.6.3
 decorator==5.1.1
 defusedxml==0.7.1
+diff-match-patch==20200713
 dill==0.3.6
+docstring-to-markdown==0.10
+docutils==0.19
 entrypoints==0.4
-executing==1.2.0
 fasteners==0.18
 fastjsonschema==2.16.2
+flake8==5.0.4
 fonttools==4.38.0
 fsspec==2022.10.0
-greenlet==2.0.0
+greenlet==2.0.0.post0
 GridDataFormats==1.0.1
-gsd==2.6.0
+gsd==2.6.1
 idna==3.4
+imagesize==1.4.1
 importlib-metadata==5.0.0
+inflection==0.5.1
+intervaltree==3.1.0
 ipydatawidgets==4.3.2
 ipykernel==6.17.0
-ipython==8.6.0
+ipython==7.34.0
 ipython-genutils==0.2.0
 ipyvolume==0.5.2
 ipywebrtc==0.6.0
 ipywidgets==8.0.2
+isort==5.10.1
+jaraco.classes==3.2.3
 jedi==0.18.1
+jeepney==0.8.0
+jellyfish==0.9.0
 Jinja2==3.1.2
+jinja2-time==0.2.0
 joblib==1.2.0
 jsonschema==4.17.0
 jupyter==1.0.0
@@ -53,19 +74,23 @@ jupyter_client==7.4.4
 jupyter_core==4.11.2
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==3.0.3
+keyring==23.11.0
 kiwisolver==1.4.4
+lazy-object-proxy==1.8.0
 locket==1.0.0
 lxml==4.9.1
 MarkupSafe==2.1.1
 matplotlib==3.6.2
 matplotlib-inline==0.1.6
+mccabe==0.7.0
 MDAnalysis==2.3.0
-mdevaluate==22.11
 mistune==2.0.4
 mmtf-python==1.1.3
+more-itertools==9.0.0
 mrcfile==1.4.3
 msgpack==1.0.4
 multiprocess==0.70.14
+mypy-extensions==0.4.3
 nbclassic==0.4.8
 nbclient==0.7.0
 nbconvert==7.2.3
@@ -75,55 +100,102 @@ networkx==2.8.8
 notebook==6.5.2
 notebook_shim==0.2.2
 numpy==1.23.4
+numpydoc==1.5.0
 packaging==21.3
 pandas==1.5.1
 pandocfilters==1.5.0
 parso==0.8.3
 partd==1.3.0
 pathos==0.3.0
+pathspec==0.10.1
 pexpect==4.8.0
 pickleshare==0.7.5
 Pillow==9.3.0
+platformdirs==2.5.2
+pluggy==1.0.0
 pox==0.3.2
 ppft==1.7.6.6
 prometheus-client==0.15.0
-prompt-toolkit==3.0.31
+prompt-toolkit==3.0.32
 psutil==5.9.3
 psycopg2-binary==2.9.5
 ptyprocess==0.7.0
-pure-eval==0.2.2
+pycodestyle==2.9.1
 pycparser==2.21
+pydocstyle==6.1.1
+pyflakes==2.5.0
 Pygments==2.13.0
+pylint==2.15.5
+pylint-venv==2.3.0
+pyls-spyder==0.4.0
 pyparsing==3.0.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.2
+PyQt5-sip==12.11.0
+PyQtWebEngine==5.15.6
+PyQtWebEngine-Qt5==5.15.2
 pyrsistent==0.19.2
 python-dateutil==2.8.2
+python-lsp-black==1.2.1
+python-lsp-jsonrpc==1.0.0
+python-lsp-server==1.6.0
+python-slugify==6.1.2
 pythreejs==2.4.1
+pytoolconfig==1.2.2
 pytz==2022.6
+pyxdg==0.28
 PyYAML==6.0
 pyzmq==24.0.1
+QDarkStyle==3.0.3
+qstylizer==0.2.2
+QtAwesome==1.2.1
 qtconsole==5.4.0
 QtPy==2.2.1
 requests==2.28.1
+rope==1.4.0
+Rtree==1.0.1
 scipy==1.9.3
+SecretStorage==3.3.3
 Send2Trash==1.8.0
 six==1.16.0
 sniffio==1.3.0
+snowballstemmer==2.2.0
+sortedcontainers==2.4.0
 soupsieve==2.3.2.post1
-SQLAlchemy==1.4.42
+Sphinx==5.3.0
-stack-data==0.6.0
+sphinxcontrib-applehelp==1.0.2
-store==0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+spyder==5.4.0
+spyder-kernels==2.4.0
+SQLAlchemy==1.4.43
 terminado==0.17.0
+text-unidecode==1.3
+textdistance==4.5.0
 threadpoolctl==3.1.0
+three-merge==0.1.1
 tinycss2==1.2.1
+toml==0.10.2
+tomli==2.0.1
+tomlkit==0.11.6
 toolz==0.12.0
 tornado==6.2
 tqdm==4.64.1
 traitlets==5.5.0
 traittypes==0.2.1
-tudplot==0.1
+typing_extensions==4.4.0
+ujson==5.5.0
 urllib3==1.26.12
+watchdog==2.1.9
 wcwidth==0.2.5
 webencodings==0.5.1
-websocket-client==1.4.1
+websocket-client==1.4.2
+whatthepatch==1.0.2
 widgetsnbextension==4.0.3
+wrapt==1.14.1
+wurlitzer==3.0.2
+yapf==0.32.0
 zipp==3.10.0