Package modernization

.gitignore

@@ -66,3 +66,6 @@ target/
 
 #Ipython Notebook
 .ipynb_checkpoints
+
+#revieweing and package modernization
+venv_ezyrb/

docs/source/conf.py

@@ -18,12 +18,22 @@
 import sphinx
 from sphinx.errors import VersionRequirementError
 import sphinx_rtd_theme
+import time
+import importlib.metadata
+
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../..'))
-import ezyrb.meta as meta
+
+
+# -- Project infirmation --------
+_DISTRIBUTION_METADATA = importlib.metadata.metadata("ezyrb")
+project = _DISTRIBUTION_METADATA["Name"]
+copyright = f'2016-{time.strftime("%Y")}, EZyRB contributors'
+author = _DISTRIBUTION_METADATA["Author"]
+
 
 # -- General configuration ------------------------------------------------
 
@@ -69,10 +79,6 @@
 # The master toctree document.
 master_doc = 'index'
 
-# General information about the project.
-project = meta.__project__
-copyright = meta.__copyright__
-author = meta.__author__
 
 # autoclass
 autoclass_content = 'both'
@@ -82,9 +88,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = meta.__version__
-# The full version, including alpha/beta/rc tags.
+version = _DISTRIBUTION_METADATA["Version"]
 release = version
+# The full version, including alpha/beta/rc tags.
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -287,7 +293,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, meta.__title__, u'EZyRB Documentation',
+    (master_doc, 'ezyrb' , u'EZyRB Documentation',
      [author], 1)
 ]
 

ezyrb/__init__.py

@@ -6,7 +6,6 @@
     'ReducedOrderModel', 'PODAE', 'RegularGrid'
 ]
 
-from .meta import *
 from .database import Database
 from .snapshot import Snapshot
 from .parameter import Parameter

pyproject.toml

@@ -0,0 +1,59 @@
+[project]
+name = "ezyrb"
+version = "1.3.1"
+description = "Easy Reduced Basis"
+readme = "README.md"
+authors = [
+    {name = "Nicola Demo", email = "demo.nicola@gmail.com"},
+    {name = "Marco Tezzele", email = "marcotez@gmail.com"},
+]
+license = { text = "MIT" }
+keywords = [
+    "pod", "interpolation", "reduced-basis", 
+    "model-order-reduction", "scientific-computing"
+]
+dependencies = [
+    "future",
+    "numpy", 
+    "scipy",
+    "matplotlib",
+    "scikit-learn>=1.0",
+    "torch",
+    "datasets"
+]
+requires-python = ">=3.8"
+
+[project.optional-dependencies]
+docs = [
+    "sphinx", 
+    "sphinx_rtd_theme"
+]
+test = [
+    "pytest", 
+    "pytest-cov"
+]
+dev = [
+    "black",
+    "pylint"
+]
+tutorial = [
+    "jupyter",
+    "notebook"
+]
+
+[project.urls]
+Homepage = "https://github.com/mathLab/EZyRB"
+Repository = "https://github.com/mathLab/EZyRB"
+
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["ezyrb*"]
+
+[tool.black]
+line-length = 80
+
+[tool.isort]
+profile = "black"

tutorials/tutorial-1.py

@@ -82,7 +82,7 @@ def hf_to_numpy(ds):
     ax[i].triplot(triang, 'b-', lw=0.1)
     cm = ax[i].tripcolor(triang, snapshots[i])
     fig.colorbar(cm, ax=ax[i])
-    ax[i].set_title('($\mu_0={:5.2f}, \mu_1={:5.2f})$'.format(*param[i]))
+    ax[i].set_title(r'($\mu_0={:5.2f}, \mu_1={:5.2f})$'.format(*param[i]))
 
 
 # First of all, we create a `Database` object from the parameters and the snapshots.

tutorials/tutorial-3.py

@@ -203,7 +203,7 @@ def wave(t, res=256):
 plt.figure(figsize=(6,4))
 plt.plot(N_modes[:10], s[:10]/np.max(s),"-s",color = "blue", label='POD')
 plt.plot(N_modes_shifted, s_shifted/np.max(s_shifted),"-o", color = "red", label='NNsPOD')
-plt.ylabel('$\sigma/\sigma_{1}$', size=15) 
+plt.ylabel(r'$\sigma/\sigma_{1}$', size=15) 
 plt.xlabel('Modes', size=15)
 plt.xlim(0, 11)
 plt.legend(fontsize=12)

utils/mathlab_versioning.py

@@ -4,8 +4,8 @@
 
 
 module = 'ezyrb'
-meta_file = os.path.join(module, 'meta.py')
-version_line = r'__version__.*=.*"(.+?)"'
+pyproject_file = 'pyproject.toml'
+version_line = r'version.*=.*"(.+?)"'
 
 
 class Version:
@@ -34,11 +34,11 @@ def __str__(self):
 
 
 def get_version():
-    with open(meta_file, 'r') as fp:
+    with open(pyproject_file, 'r') as fp:
         content = fp.read()
 
     try:
-        found = re.search(r'__version__.*=.*"(.+?)"', content).group(1)
+        found = re.search(r'version.*=.*"(.+?)"', content).group(1)
     except AttributeError:
         pass
 
@@ -48,13 +48,13 @@ def get_version():
 
 
 def set_version(version):
-    with open(meta_file, 'r') as fp:
+    with open(pyproject_file, 'r') as fp:
         content = fp.read()
 
-    line_string = '__version__ = "{}"'.format(version)
-    text_after = re.sub('__version__.*=.*"(.+?)"', line_string, content)
+    line_string = 'version = "{}"'.format(version)
+    text_after = re.sub('version.*=.*"(.+?)"', line_string, content)
 
-    with open(meta_file, 'w') as fp:
+    with open(pyproject_file, 'w') as fp:
         fp.write(text_after)