Update project setup

.gitignore

@@ -74,7 +74,7 @@ odmltables/gui/graphics/*.dvi
 odmltables/gui/graphics/*.ps
 odmltables/gui/graphics/*.txt
 odmltables/gui/graphics/*.tex.backup
-odmltables/gui/testfiles/*
+src/odmltables/gui/testfiles/*
 doc/build/*
 doc/_build/*
 doc/requirements*.rst

doc/conf.py

@@ -13,18 +13,17 @@
 # serve to show the default.
 
 import sys
-import glob
 import subprocess
 import os
-
+import tomllib
 
 # 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('.'))
 sys.path.insert(0, os.path.abspath('../src'))
 sys.path.insert(0, os.path.abspath('../../python-odml/'))
-sys.path.insert(0, os.path.abspath('../odmltables'))
+sys.path.insert(0, os.path.abspath('../src/odmltables'))
 sys.path.insert(0, os.path.abspath('..'))
 
 # installing current odMLtables version
@@ -33,25 +32,25 @@
 output, error = process.communicate()
 
 import odmltables
+
 VERSION = odmltables.VERSION
 
 # reformatting requirements files to be automatically included in docu
-requirement_files = glob.glob('../requirements*.txt')
-for requirement_file in requirement_files:
-    with open(requirement_file, 'r') as f:
-        lines = f.readlines()
-    # listify and increase readability
-    for line_id in range(len(lines)):
-        lines[line_id] = '* ' + lines[line_id]
-        lines[line_id] = lines[line_id].replace(';', ' in case of ')
-    new_filename = f'{os.path.splitext(os.path.basename(requirement_file))[0]}.rst'
-    with open(new_filename, 'w+') as f:
-        f.writelines(lines)
-
-
+with open("../pyproject.toml", "rb") as f:
+    data = tomllib.load(f)
 
+def format_dependencies(dependency_list):
+    # format a list of dependencies into a block text list
+    formatted_dependencies = '\n* '.join(dependency_list).replace(';', ' in case of ')
+    return formatted_dependencies
 
+dependencies = data["project"]["dependencies"]
+with open('requirements.rst', 'w+') as f:
+    f.write(format_dependencies(dependencies))
 
+for option, optional_dependencies in data["project"]["optional-dependencies"].items():
+    with open(f'requirements_{option}.rst', 'w+') as f:
+        f.write(format_dependencies(optional_dependencies))
 
 
 # -- General configuration ------------------------------------------------

doc/environment.yml

@@ -1,11 +1,14 @@
 name: odmltables
+channels:
+  - conda-forge
+  - free
+  - anaconda
 dependencies:
-- python=3.7
-- setuptools
-- snowballstemmer
-- sphinx
-- sphinx_rtd_theme
-- pip
-- pip:
-  - odml
-  - sphinx-rtd-theme
+  - python==3.11
+  - setuptools
+  - snowballstemmer
+  - sphinx
+  - sphinx_rtd_theme
+  - pip
+  - pip:
+    - odml

doc/tutorial.rst

@@ -15,10 +15,11 @@ version `1.0 <https://github.com/G-Node/odml-terminologies/blob/master/v1.0/odml
 the `G-Node <http://www.g-node.org/projects/odml>`_.
 
 
-In addition to the detailed step-by-step instructions presented here, there are also two **interactive tutorials** available as `jupyter notebooks`_. Both tutorials can be directly executed using binder_ or run locally from the odmltables sources (:any:`tutorials/tutorial-1_scenarios/demo_scenarios.ipynb`) folder. The first notebook (|notebook1|) is giving a quick overview on how odMLtables can be used in a metadata workflow by presenting a number of small application scenarios. The second notebook (|notebook2|) shows the usage of odMLtables for handling large metadata collections and is based on two published experimental datasets.
+In addition to the detailed step-by-step instructions presented here, there are also two **interactive tutorials** available as `jupyter notebooks`_. Both tutorials can be directly executed using binder_ or run locally from the odmltables `tutorial folder`_. The first notebook (|notebook1|) is giving a quick overview on how odMLtables can be used in a metadata workflow by presenting a number of small application scenarios. The second notebook (|notebook2|) shows the usage of odMLtables for handling large metadata collections and is based on two published experimental datasets.
 
 .. _binder: https://mybinder.org/
 .. _jupyter notebooks: http://jupyter.org/
+.. _tutorial folder: https://github.com/INM-6/python-odmltables/tree/master/tutorials
 
 .. |notebook1|  image:: https://mybinder.org/badge.svg
   :target: https://mybinder.org/v2/gh/inm-6/python-odmltables/master?filepath=tutorials%2Ftutorial-1_scenarios%2Fdemo_scenarios.ipynb

examples/example1/example1.py

@@ -17,7 +17,7 @@ def run_example():
 
 def setup_example():
     # We are using the same csv table as used in the tutorial
-    filename = '../../doc/source/csv/example1-2.csv'
+    filename = 'example1-2.csv'
 
     xlstable = odml_xls_table.OdmlXlsTable()
     xlstable.load_from_csv_table(filename)

examples/example2/example2.py

@@ -2,7 +2,6 @@
 import datetime
 import odml.base
 import odmltables.odml_xls_table as odml_xls_table
-from odmltables.xls_style import XlsStyle
 
 pre_enriched_file = 'example2-1.odml'
 

examples/example3/example3.py

@@ -1,7 +1,6 @@
 import datetime
 
 import odml
-from odml import DType
 import odmltables.odml_xls_table as odml_xls_table
 
 

pyproject.toml

@@ -0,0 +1,78 @@
+[project]
+name = "odmltables"
+version = "1.0.1dev"
+authors = [
+    {name = "odMLtables authors and contributors"},
+    {email = "[email protected]"}
+]
+description = "An interface to convert odML structues to and from table-like representations, such as spreadsheets"
+readme = "README.rst"
+requires-python = ">=3.6"
+license = {text = "BSD 3-Clause License"}
+keywords = ["odml", "excel", "metadata management"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+]
+
+dependencies = [
+    "xlrd >= 0.9.4",
+    "xlwt >= 1.0.0",
+    "numpy >= 1.8.2",
+    "quantities >= 0.10.1",
+    "odml >= 1.4.2",
+    "future >= 0.16.0",
+    "argparse >= 1.0.0",
+]
+
+[project.urls]
+documentation = "http://odmltables.readthedocs.io/"
+repository = "https://github.com/INM-6/python-odmltables"
+download = "http://pypi.python.org/pypi/odmltables"
+
+
+[build-system]
+requires = ["setuptools>=62.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+odmltables = ["gui/graphics/*", "logo/*"]
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+addopts = "-ra -q"
+testpaths = [
+    "tests",
+]
+pythonpath = [
+  "src"
+]
+
+[project.gui-scripts]
+odmltables = "odmltables.gui.main:parse_args"
+
+[project.optional-dependencies]
+
+doc = [
+    "numpydoc>=0.5.0",
+    "sphinx>=1.2.2",
+]
+
+gui = ["PyQt5>=5.0.0"]
+
+test = ["pytest>=3.0.0"]

odmltables/__init__.py → src/odmltables/__init__.py

@@ -1,8 +1,7 @@
-import os.path
-
-with open(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'VERSION.txt')) as version_file:
-    VERSION = version_file.read().strip()
-
+import importlib.metadata
+# this need to be at the begining because some sub module will need the version
+__version__ = importlib.metadata.version("odmltables")
+VERSION = __version__
 
 # -*- coding: utf-8 -*-
 """
@@ -15,9 +14,4 @@
 .. autoclass:: odmltables.compare_section_csv_table.CompareSectionCsvTable
 """
 
-
-from odmltables.odml_table import OdmlTable
 from odmltables.odml_csv_table import OdmlCsvTable
-from odmltables.odml_xls_table import OdmlXlsTable
-from odmltables.compare_section_csv_table import CompareSectionCsvTable
-from odmltables.compare_section_xls_table import CompareSectionXlsTable

odmltables/gui/compsectionpages.py → src/odmltables/gui/compsectionpages.py

@@ -9,10 +9,9 @@
 import subprocess
 
 from PyQt5.QtWidgets import (QVBoxLayout, QHBoxLayout, QMessageBox,
-                         QLineEdit, QPushButton, QLabel, QGroupBox,
-                         QGridLayout, QTreeWidget, QTreeWidgetItem,
-                         QToolButton, QFileDialog, QCheckBox, QComboBox,
-                         QFrame, QSizePolicy, QRadioButton)
+                             QLineEdit, QPushButton, QLabel, QGroupBox,
+                             QGridLayout, QTreeWidget, QTreeWidgetItem,
+                             QToolButton, QFileDialog, QCheckBox, QRadioButton)
 
 from PyQt5.QtCore import Qt
 

odmltables/gui/converterpages.py → src/odmltables/gui/converterpages.py

@@ -12,7 +12,7 @@
 import PyQt5.QtGui as Qtg
 
 from .pageutils import QIWizardPage, clearLayout, get_property, get_rgb, shorten_path
-from odmltables import odml_table, odml_xls_table, odml_csv_table, xls_style
+from .. import odml_csv_table, odml_xls_table, xls_style, odml_table
 
 
 class LoadFilePage(QIWizardPage):

odmltables/gui/filterpages.py → src/odmltables/gui/filterpages.py

@@ -16,7 +16,7 @@
 from PyQt5.QtCore import Qt
 import PyQt5.QtWidgets as Qtw
 
-from odmltables import odml_table
+from .. import odml_table
 from .pageutils import QIWizardPage, clearLayout, shorten_path
 
 

odmltables/gui/generatetemplatepages.py → src/odmltables/gui/generatetemplatepages.py

@@ -12,7 +12,7 @@
 from PyQt5.QtCore import Qt
 
 import odml
-from odmltables import odml_table, odml_xls_table, odml_csv_table, xls_style
+from .. import odml_xls_table, odml_table
 from .pageutils import QIWizardPage, clearLayout, shorten_path
 
 mandatory_headers = ['Path to Section',