Merge pull request #27 from amepproject/release-1.0.x

merge release 1.0.x into develop
amepproject · May 22, 2024 · 42b6b40 · 42b6b40
2 parents 67d3d17 + 1a54f37
commit 42b6b40
Show file tree

Hide file tree

Showing 23 changed files with 186 additions and 80 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,19 @@
 All notable changes to **AMEP** will be documented in this file. **AMEP** 
 adheres to [semantic versioning](https://semver.org/).
 
+## AMEP 1.0.2 (22 Mai 2024)
+
+### Bug fixes:
+
+* `fps` can now be set by the user in `amep.plot.animate_trajectory`
+* bug in `amep.evaluate.MSD` related to incorrect data availability checks fixed
+
+### Contributors:
+
+* Lukas Hecht
+
+
+
 ## AMEP 1.0.1 (22 Apr 2024)
 
 ### Bug fixes:

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+message: "If you use AMEP for a project that leads to a scientific publication, please acknowledge the use of AMEP within the body of your publication by citing L. Hecht, K.-R. Dormann, K. L. Spanheimer, M. Ebrahimi, M. Cordts, S. Mandal, A. K. Mukhopadhyay, and B. Liebchen, AMEP: The Active Matter Evaluation Package for Python, arXiv [Cond-Mat.Soft] (2024). Available at: http://arxiv.org/abs/2404.16533."
+title: 'AMEP: The Active Matter Evaluation Package'
+authors:
+  - name: "Lukas Hecht and the AMEP development team"
+    website: "https://amepproject.de/"
+type: software
+url: "https://amepproject.de/"
+repository-code: "https://github.com/amepproject/amep"
+preferred-citation:
+  type: article
+  authors:
+    - family-names: "Hecht"
+      given-names: "Lukas"
+      orcid: "https://orcid.org/0000-0002-9619-4991"
+    - family-names: "Dormann"
+      given-names: "Kay-Robert"
+    - family-names: "Spanheimer"
+      given-names: "Kai Luca"
+    - family-names: "Ebrahimi"
+      given-names: "Mahdieh"
+    - family-names: "Cordts"
+      given-names: "Malte"
+    - family-names: "Mandal"
+      given-names: "Suvendu"
+    - family-names: "Mukhopadhyay"
+      given-names: "Aritra K."
+    - family-names: "Liebchen"
+      given-names: "Benno"
+      orcid: "https://orcid.org/0000-0002-7647-6430"
+  title: "AMEP: The Active Matter Evaluation Package for Python"
+  year: 2024
+  doi: "10.48550/arXiv.2404.16533"
+  journal: "arXiv"
+  url: "https://arxiv.org/abs/2404.16533"
diff --git a/README.md b/README.md
@@ -5,6 +5,8 @@
 [![Pepy Total Downlods](https://img.shields.io/pepy/dt/amep?label=pypi%7Cdownloads)](https://pypi.org/project/amep/)
 [![Conda Downloads](https://img.shields.io/conda/d/conda-forge/amep)](https://anaconda.org/conda-forge/amep)
 [![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/amepproject/amep/test.yml?label=pipeline)](https://github.com/amepproject/amep/actions)
+[![Static Badge](https://img.shields.io/badge/arXiv-2404.16533-brown)](https://doi.org/10.48550/arXiv.2404.16533)
+
 
 <center><img src="https://raw.githubusercontent.com/amepproject/amep/main/doc/source/_static/images/amep-logo_v2.png" alt="amep logo" width="200" height="200"/></center>
 
@@ -144,6 +146,40 @@ Anaconda installation path.
 to download FFmpeg and to get further information on how to install FFmpeg on your machine.
 
 
+# Citation
+
+If you use **AMEP** for a project that leads to a scientific publication, please acknowledge 
+the use of **AMEP** within the body of your publication for example by copying or adapting 
+the following formulation:
+
+*Data analysis for this publication utilized the AMEP library [1].*
+
+> [1] L. Hecht, K.-R. Dormann, K. L. Spanheimer, M. Ebrahimi, M. Cordts, S. Mandal, 
+>     A. K. Mukhopadhyay, and B. Liebchen, AMEP: The Active Matter Evaluation Package for Python, 
+>     *arXiv [Cond-Mat.Soft]* (2024). Available at: http://arxiv.org/abs/2404.16533.
+
+The pre-print is freely available on [arXiv](https://arxiv.org/abs/2404.16533). To cite this reference, 
+you can use the following BibTeX entry:
+
+```bibtex
+@misc{hecht2024amep,
+    title = {AMEP: The Active Matter Evaluation Package for Python}, 
+    author = {Lukas Hecht and 
+              Kay-Robert Dormann and 
+              Kai Luca Spanheimer and 
+              Mahdieh Ebrahimi and 
+              Malte Cordts and 
+              Suvendu Mandal and 
+              Aritra K. Mukhopadhyay and 
+              Benno Liebchen},
+    year = {2024},
+    eprint = {2404.16533},
+    archivePrefix = {arXiv},
+    primaryClass = {cond-mat.soft}
+}
+```
+
+
 # Getting started
 
 The following example briefly demonstrates the **AMEP** workflow. A typical 

diff --git a/amep/_version.py b/amep/_version.py
@@ -20,4 +20,4 @@
 """
 AMEP version number.
 """
-__version__ = "1.0.1"
+__version__ = "1.0.2"
diff --git a/amep/evaluate.py b/amep/evaluate.py
@@ -3802,35 +3802,41 @@ def __init__(
 
         # get reference frame at time t0:
         self.__frame0 = self.__traj[self.__nskip]
-
+        
         # check data availability
-        if self.__use_nojump and self.__traj[0].nojump_coords() is None:
-            raise ValueError(
-                'No nojump coordinates available. Call traj.nojump() '\
-                'to calculate the nojump coordinates.'
-            )
-        elif self.__pbc and self.__traj[0].unwrapped_coords() is None\
-        and self.__traj[0].nojump_coords() is None:
-            raise ValueError(
-                'Neither unwrapped nor nojump coordinates are available. '\
-                'Call traj.nojump() to calculate the nojump coordinates or '\
-                'do not apply periodic boundary conditions.'
-            )
-        else:
-            # get mode
-            if self.__use_nojump or\
-            (self.__pbc and self.__traj[0].unwrapped_coords() is None):
-                self.__mode = 'nojump'
-            elif self.__pbc and self.__traj[0].unwrapped_coords() is not None:
-                self.__mode = 'unwrapped'
+        if self.__pbc:
+            if self.__use_nojump:
+                try:
+                    a = self.__traj[0].nojump_coords()
+                except:
+                    raise ValueError(
+                        'No nojump coordinates available. Call traj.nojump() '\
+                        'to calculate the nojump coordinates.'
+                    )
             else:
-                self.__mode = 'normal'
-            # calculation
-            self.__frames, self.__avg, self.__indices = average_func(
-                self.__compute, self.__traj, skip=self.__skip,
-                nr=self.__nav, indices=True
-            )
-            self.__times = self.__traj.times[self.__indices]
+                try:
+                    a = self.__traj[0].unwrapped_coords()
+                except:
+                    raise ValueError(
+                        'There are no unwrapped coordinates available. '\
+                        'Please set use_nojump=True to use nojump coordinates '\
+                        'instead or do not apply periodic boundary conditions.'
+                    )
+        # get mode
+        if self.__pbc and self.__use_nojump:
+            self.__mode = 'nojump'
+        elif self.__pbc:
+            self.__mode = 'unwrapped'
+        else:
+            self.__mode = 'normal'
+
+        # calculation
+        self.__frames, self.__avg, self.__indices = average_func(
+            self.__compute, self.__traj, skip=self.__skip,
+            nr=self.__nav, indices=True
+        )
+        self.__times = self.__traj.times[self.__indices]
+
 
     def __compute(self, frame):
         r'''

diff --git a/amep/plot.py b/amep/plot.py
@@ -1426,7 +1426,7 @@ def animate_trajectory(
         formatter: Callable[[mpl.axes.Axes,], None] | None = None,
         painter: object | None = None,
         title: str = '', figsize: tuple[float, float] | None = None,
-        start: float = 0.0, stop: float = 1.0, nth: int = 1,
+        start: float = 0.0, stop: float = 1.0, nth: int = 1, fps: int = 10,
         verbose: bool = False, **kwargs) -> None:
     r'''Create a video from a trajectory.
 
@@ -1490,6 +1490,8 @@ def animate_trajectory(
         larger than `start`. The default is 1.0.
     nth : int, optional
         Use each nth frame to make the animate. The default is 1.
+    fps: int, optional
+        The frames per second of the video. The default is 10.
     verbose : bool, optional
         If True, runtime information is printed. The default is False.
     **kwargs
@@ -1668,6 +1670,7 @@ def animate(index: int) -> list:
     with tqdm(total = len(indices)) as pbar:
         anim.save(
             outfile,
+            fps = fps,
             progress_callback = lambda frameindex, nframes: pbar.update()
         )
     plt.close(fig)

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -9,7 +9,7 @@
 project = 'AMEP'
 copyright = '2023-2024, Lukas Hecht, Kay-Robert Dormann, Kai Luca Spanheimer'
 author = 'Lukas Hecht, Kay-Robert Dormann, Kai Luca Spanheimer'
-release = '1.0.1'
+release = '1.0.2'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -8,7 +8,7 @@ AMEP documentation
 
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
-   :start-line: 10
+   :start-line: 11
 
 Table of Contents
 =================

diff --git a/doc/source/user_guide/howto_cite.rst b/doc/source/user_guide/howto_cite.rst
@@ -2,12 +2,33 @@
 How to cite **AMEP**
 =====================
 
-Please acknowledge the use of this software within the body of your publication for example by copying or adapting the following formulation:
+If you use **AMEP** for a project that leads to a scientific publication, please acknowledge 
+the use of **AMEP** within the body of your publication for example by copying or adapting 
+the following formulation:
 
 *Data analysis for this publication utilized the AMEP library [1].*
 
-To cite **AMEP**, you can use the following BibTeX entry:
+| [1] L. Hecht, K.-R. Dormann, K. L. Spanheimer, M. Ebrahimi, M. Cordts, S. Mandal, 
+|     A. K. Mukhopadhyay, and B. Liebchen, AMEP: The Active Matter Evaluation Package for Python, 
+|     *arXiv [Cond-Mat.Soft]* (2024). Available at: http://arxiv.org/abs/2404.16533.
+
+The pre-print is freely available on `arXiv <https://arxiv.org/abs/2404.16533>`_. To cite this reference, 
+you can use the following BibTeX entry:
 
 .. code-block:: bibtex
 
-   coming soon...
+   @misc{hecht2024amep,
+        title = {AMEP: The Active Matter Evaluation Package for Python}, 
+        author = {Lukas Hecht and 
+                  Kay-Robert Dormann and 
+                  Kai Luca Spanheimer and 
+                  Mahdieh Ebrahimi and 
+                  Malte Cordts and 
+                  Suvendu Mandal and 
+                  Aritra K. Mukhopadhyay and 
+                  Benno Liebchen},
+        year = {2024},
+        eprint = {2404.16533},
+        archivePrefix = {arXiv},
+        primaryClass = {cond-mat.soft}
+    }
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,9 +1,9 @@
 [project]
 name = "amep"
-version = "1.0.1"
+version = "1.0.2"
 license = {file="LICENSE"}
 authors = [
-	{name = "Lukas Hecht", email = "lukas.hecht@pkm.tu-darmstadt.de"},
+    {name = "Lukas Hecht", email = "lukas.hecht@pkm.tu-darmstadt.de"},
 ]
 description = "Active Matter Evaluation Package for data analysis of active matter simulations"
 readme = "README.md"
@@ -17,26 +17,26 @@ keywords = [
 ]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
-	"Intended Audience :: Science/Research",
-	"Intended Audience :: Education",
-	"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
-	"Natural Language :: English",
-	"Operating System :: OS Independent",
-	"Programming Language :: Python :: 3",
-	"Programming Language :: Python :: 3.10",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-	"Topic :: Scientific/Engineering :: Physics",
-	"Topic :: Scientific/Engineering :: Visualization",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
-	"h5py >= 3.7.0",
-	"matplotlib >= 3.6.2",
-	"numba >= 0.56.4",
-	"numpy >= 1.21.6",
-	"scipy >= 1.10.0",
-	"scikit-image >= 0.20.0",
-	"tqdm >= 4.65.0"
+    "h5py >= 3.7.0",
+    "matplotlib >= 3.6.2",
+    "numba >= 0.56.4",
+    "numpy >= 1.21.6",
+    "scipy >= 1.10.0",
+    "scikit-image >= 0.20.0",
+    "tqdm >= 4.65.0"
 ]
 
 [project.urls]

diff --git a/test/test_base.py b/test/test_base.py
@@ -25,8 +25,6 @@
 # =============================================================================
 import numpy as np
 import unittest
-import sys
-sys.path.append('/Lukas/Documents/17_Promotion/10_scripts/development/amep-dev')
 import os
 import amep
 

diff --git a/test/test_continuum.py b/test/test_continuum.py
@@ -146,3 +146,7 @@ def test_cluster(self):
         )
         plot.field(axe[2], labels, *trajectory[-1].grid)
         fig.savefig(PLOT_DIR/"Cluster_test.pdf")
+
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/test/test_evaluate.py b/test/test_evaluate.py
@@ -81,10 +81,10 @@ def setUpClass(cls):
 
     def test_cluster_growth(self):
         self.assertTrue((ClusterGrowth(self.field_trajs[1], scale=1.5, cutoff=0.8,
-                                       ftype="c", mode="mean").frames <=
+                                       ftype="c", mode="mean").frames.sum() <=
                         ClusterGrowth(self.field_trajs[1], scale=1.5, cutoff=0.8,
                                       ftype="c",
-                                      mode="weighted mean").frames).all())
+                                      mode="weighted mean").frames.sum()))
         self.assertTrue((ClusterGrowth(self.field_trajs[1],
                                        ftype="c",
                                        mode="largest").frames >= 0).all())

diff --git a/test/test_functions.py b/test/test_functions.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # =============================================================================
-# Copyright (C) 2023 Lukas Hecht and the AMEP development team.
+# Copyright (C) 2023-2024 Lukas Hecht and the AMEP development team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -50,3 +50,6 @@ def test_gaussian(self):
         new_x = x_vec*0.3 + 2
         axs.plot(new_x, gauss.generate(new_x), label="fit")
         fig.savefig(PLOT_DIR/Path("test_gaussian.pdf"))
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/test/test_load.py b/test/test_load.py
@@ -24,11 +24,9 @@
 # IMPORT MODULES
 # =============================================================================
 import unittest
-import sys
 from zipfile import ZipFile
 from requests import get
 from pathlib import Path
-sys.path.append('/Lukas/Documents/17_Promotion/10_scripts/development/amep-dev')
 import amep
 
 SERVER_URL: str = "https://kuno.fkp.physik.tu-darmstadt.de/d/a3d9887b8a5747e0a56e/files/?p=/"

diff --git a/test/test_order.py b/test/test_order.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # =============================================================================
-# Copyright (C) 2023 Lukas Hecht and the AMEP development team.
+# Copyright (C) 2023-2024 Lukas Hecht and the AMEP development team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -25,8 +25,6 @@
 # =============================================================================
 import numpy as np
 import unittest
-import sys
-sys.path.append('/Lukas/Documents/17_Promotion/10_scripts/development/amep-dev')
 import amep
 
 # =============================================================================