Merge pull request #2 from amepproject/release-v1.0.0

Release v1.0.0

.gitignore

@@ -16,18 +16,7 @@
 *.zip
 
 # full directories
-tests/
-releases/
-backups/
-eval/
-figures/
-logo/
-toadd/
-files/
-pyh5md/
-projectweek/
-parallelization/
-hdf5/
+amep.egg-info/
 
 # compiled
 __pycache__/
@@ -51,7 +40,6 @@ config/
 build/
 
 # Test and example directories and files
-figures
 test/data
 test/.coverage
 test/coverage.xml

AUTHORS

@@ -28,6 +28,7 @@ Chronological list of authors
   - Aritra Mukhopadhyay
   - Mahdieh Ebrahimi
   - Suvendu Mandal
+  - Benno Liebchen
   - Malte Cordts
   - Lukas Walter
 
@@ -36,4 +37,5 @@ Chronological list of authors
   - Kay-Robert Dormann
   - Kai Luca Spanheimer
   - Aritra Mukhopadhyay
-  - Mahdieh Ebrahimi
+  - Mahdieh Ebrahimi
+  - Benno Liebchen

CHANGELOG.md

@@ -3,11 +3,12 @@
 All notable changes to **AMEP** will be documented in this file. **AMEP** 
 adheres to [semantic versioning](https://semver.org/).
 
-## AMEP 1.0.0-dev
+## AMEP 1.0.0  (21 Mar 2024)
 
 This is the first public version of **AMEP**. It fully integrates the analysis 
 of continuum simulation data, fixes various bugs of version 0.5.0, and provides 
-useful new features. 
+useful new features. It is also the first version that can be installed via 
+conda and pip.
 
 ### New features:
 

MANIFEST.in

@@ -0,0 +1,3 @@
+prune amep.egg-info
+prune doc
+prune test

README.md

@@ -1,6 +1,6 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![GitHub Discussions](https://img.shields.io/github/discussions/amepproject/amep)](https://github.com/amepproject/amep/discussions)
-![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Famepproject%2Famep%2Fdoc%2Fupdate%2Fpyproject.toml)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Famepproject%2Famep%2Fmain%2Fpyproject.toml)
 [![Static Badge](https://img.shields.io/badge/documentation-amepproject.de-blue)](https://amepproject.de)
 
 <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>
@@ -116,13 +116,13 @@ Anaconda installation path.
 
 ## Installation via pip
 
-The installation via `pip` is recommended. Please ensure that the Python 
-modules `setuptools` and `build` are installed in your Python environment. 
-Then, download the latest version from 
-[https://github.com/amepproject/amep](https://github.com/amepproject/amep) 
-and install it via `pip install ./amep-<version>.targ.gz`. Alternatively, you 
-can also install **AMEP** from source by `pip install -e amep` while being one 
-directory above the source.
+**AMEP** can be simply installed using `pip`: 
+
+```bash
+pip install amep
+```
+
+The installation via `pip` is recommended.
 
 ## FFmpeg
 
@@ -262,6 +262,7 @@ The following people contributed to **AMEP**:
 - Aritra Mukhopadhyay (developer)
 - Mahdieh Ebrahimi (developer)
 - Suvendu Mandal (developer)
+- Benno Liebchen (planning)
 - Lukas Walter (former developer)
 - Malte Cordts (former developer)
 

amep/_version.py

@@ -20,4 +20,4 @@
 """
 AMEP version number.
 """
-__version__ = '1.0.0-dev'
+__version__ = "1.0.0"

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 = '1.0.0-dev'
+release = '1.0.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -58,7 +58,7 @@
                 # Label for this link
                 "name": "PyPI",
                 # URL where the link will redirect
-                "url": "https://pypi.org/",  # required
+                "url": "https://pypi.org/project/amep/",  # required
                 # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
                 "icon": "fa-brands fa-python",
                 # The type of image to be used (see below for details)

doc/source/gettingstarted/installation.rst

@@ -35,10 +35,13 @@ you can alternatively add the ``amep`` directory to ``Lib/site-packages`` in the
 Installation via pip
 --------------------
 
+**AMEP** can be simply installed via pip:
+
+.. code-block:: bash
+
+    pip install amep
+
 The installation via ``pip`` is recommended.
-Please ensure that the Python modules ``setuptools`` and ``build`` are installed in your Python environment.
-Then, download the latest version from https://github.com/amepproject/amep and install it via ``pip install ./amep-<version>.tar.gz``.
-Alternatively, you can can also install from source by ``pip install -e .`` while being inside the unpacked source directory.
 
 ------
 FFmpeg

pyproject.toml

@@ -1,41 +1,73 @@
 [project]
-name="amep"
-version="1.0.0-dev"
-license={file="LICENSE"}
-authors=[
-	{name="Lukas Hecht", email="lukas.hecht@pkm.tu-darmstadt.de"},
-	]
-description="""The AMEP (Active Matter Evaluation Package) Python library is a powerful tool for analyzing data from molecular-dynamics (MD), Brownian-dynamics (BD), and continuum simulations. It comprises various methods to analyze structural and dynamical properties of condensed matter systems in general and active matter systems in particular. AMEP is exclusively built on Python, and therefore, it is easy to modify and allows to easily add user-defined methods. AMEP provides an efficient data format for saving both simulation data and analysis results based on the HDF5 file format. To be fast and usable on modern HPC (High Performance Computing) hardware, the methods are optimized to run also in parallel."""
-readme="README.md"
-requires-python=">=3.10.0"
-keywords=["active matter", "soft matter", "physics", "data analysis"]
-classifiers=[
+name = "amep"
+version = "1.0.0"
+license = {file="LICENSE"}
+authors = [
+	{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"
+requires-python = ">=3.10"
+keywords = [
+    "active matter",
+    "soft matter",
+    "physics",
+    "data analysis",
+    "computational physics",
+]
+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",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 	"Topic :: Scientific/Engineering :: Physics",
-	"Topic :: Scientific/Engineering :: Visualization"
+	"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"
+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"
 ]
+
 [project.urls]
-repository="https://git.rwth-aachen.de/liebchengroup/aghecht/amep"
+"Homepage" = "https://amepproject.de/"
+"Issues" = "https://github.com/amepproject/amep/issues"
+"Repository" = "https://github.com/amepproject/amep"
+"Documentation" = "https://amepproject.de/"
+"Source Code" = "https://github.com/amepproject/amep"
+"Forum" = "https://github.com/amepproject/amep/discussions"
+"Changelog" = "https://github.com/amepproject/amep/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+# Should be a copy of the build dependencies below.
+dev = [
+    "setuptools >= 64",
+]
 
 [build-system]
-requires=["setuptools"]
-build-backend="setuptools.build_meta"
+requires = ["setuptools >= 64"]
+build-backend = "setuptools.build_meta"
+
 [tool.setuptools.packages]
-find={}
+find = {}
+
 [options.packages.find]
-include=["amep"]
-exclude=["hdf5", "config"]
+include = ["amep"]
+exclude = [
+    "doc",
+    "examples",
+    "test",
+]
+
 [tool.setuptools.package-data]
 "amep.styles" = ["*.mplstyle"]