From 86297389e775cc531987bd5a7a6c1c52c8c1a808 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= <fccoelho@gmail.com>
Date: Thu, 19 Dec 2024 06:43:00 -0300
Subject: [PATCH] improved pyproject.toml

---
 .idea/workspace.xml            | 67 ++++++++++++++------------
 condarecipe/epigrass/meta.yaml | 88 ----------------------------------
 pyproject.toml                 | 18 +++++++
 setup.cfg                      |  5 --
 setup.py                       | 34 -------------
 5 files changed, 55 insertions(+), 157 deletions(-)
 delete mode 100644 condarecipe/epigrass/meta.yaml
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 23a2886..ede6ca8 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -31,9 +31,12 @@
     <select />
   </component>
   <component name="ChangeListManager">
-    <list default="true" id="991a2459-6152-47ff-ac53-e228bf684060" name="Default" comment="fixed many bugs">
+    <list default="true" id="991a2459-6152-47ff-ac53-e228bf684060" name="Default" comment="updated the READme">
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/README.md" beforeDir="false" afterPath="$PROJECT_DIR$/README.md" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/condarecipe/epigrass/meta.yaml" beforeDir="false" />
+      <change beforePath="$PROJECT_DIR$/pyproject.toml" beforeDir="false" afterPath="$PROJECT_DIR$/pyproject.toml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/setup.cfg" beforeDir="false" />
+      <change beforePath="$PROJECT_DIR$/setup.py" beforeDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -88,9 +91,9 @@
   <component name="ProblemsViewState">
     <option name="selectedIndex" value="1" />
   </component>
-  <component name="ProjectColorInfo"><![CDATA[{
-  "associatedIndex": 4
-}]]></component>
+  <component name="ProjectColorInfo">{
+  &quot;associatedIndex&quot;: 4
+}</component>
   <component name="ProjectId" id="1Q9PACfz950Hmw7id8gkPEq5TWz" />
   <component name="ProjectLevelVcsManager" settingsEditedManually="true" />
   <component name="ProjectReloadState">
@@ -100,28 +103,31 @@
     <option name="hideEmptyMiddlePackages" value="true" />
     <option name="showLibraryContents" value="true" />
   </component>
-  <component name="PropertiesComponent"><![CDATA[{
-  "keyToString": {
-    "Python tests.Python tests in test_epigdal.py.executor": "Run",
-    "Python tests.Python tests in test_manager.py.executor": "Run",
-    "Python tests.Python tests in test_simobj.py.executor": "Run",
-    "Python tests.Python tests in tests.executor": "Run",
-    "Python.Epigrass.manager:main.executor": "Run",
-    "Python.epipanel.executor": "Run",
-    "Python.epirunner.executor": "Run",
-    "Python.rio.executor": "Run",
-    "RunOnceActivity.ShowReadmeOnStart": "true",
-    "RunOnceActivity.git.unshallow": "true",
-    "git-widget-placeholder": "master",
-    "last_opened_file_path": "/home/fccoelho/Documentos/Projects_Software/epigrass/.venv/bin/epirunner",
-    "node.js.detected.package.eslint": "true",
-    "node.js.detected.package.tslint": "true",
-    "node.js.selected.package.eslint": "(autodetect)",
-    "node.js.selected.package.tslint": "(autodetect)",
-    "nodejs_package_manager_path": "npm",
-    "vue.rearranger.settings.migration": "true"
+  <component name="PropertiesComponent">{
+  &quot;keyToString&quot;: {
+    &quot;Python tests.Python tests in test_epigdal.py.executor&quot;: &quot;Run&quot;,
+    &quot;Python tests.Python tests in test_manager.py.executor&quot;: &quot;Run&quot;,
+    &quot;Python tests.Python tests in test_simobj.py.executor&quot;: &quot;Run&quot;,
+    &quot;Python tests.Python tests in tests.executor&quot;: &quot;Run&quot;,
+    &quot;Python.Epigrass.manager:main.executor&quot;: &quot;Run&quot;,
+    &quot;Python.epipanel.executor&quot;: &quot;Run&quot;,
+    &quot;Python.epirunner.executor&quot;: &quot;Run&quot;,
+    &quot;Python.rio.executor&quot;: &quot;Run&quot;,
+    &quot;RunOnceActivity.ShowReadmeOnStart&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.git.unshallow&quot;: &quot;true&quot;,
+    &quot;git-widget-placeholder&quot;: &quot;master&quot;,
+    &quot;last_opened_file_path&quot;: &quot;/home/fccoelho/Documentos/Projects_Software/epigrass/.venv/bin/epirunner&quot;,
+    &quot;node.js.detected.package.eslint&quot;: &quot;true&quot;,
+    &quot;node.js.detected.package.tslint&quot;: &quot;true&quot;,
+    &quot;node.js.selected.package.eslint&quot;: &quot;(autodetect)&quot;,
+    &quot;node.js.selected.package.tslint&quot;: &quot;(autodetect)&quot;,
+    &quot;nodejs_package_manager_path&quot;: &quot;npm&quot;,
+    &quot;vue.rearranger.settings.migration&quot;: &quot;true&quot;
+  },
+  &quot;keyToStringList&quot;: {
+    &quot;stardust.markdown.MarkdownSplitEditorSuppressor:keyList&quot;: []
   }
-}]]></component>
+}</component>
   <component name="PyDebuggerOptionsProvider">
     <option name="mySaveCallSignatures" value="true" />
     <option name="myDropIntoDebuggerOnFailedTests" value="true" />
@@ -534,7 +540,8 @@
       <workItem from="1608401847529" duration="81000" />
       <workItem from="1613904327797" duration="8348000" />
       <workItem from="1615726523518" duration="5251000" />
-      <workItem from="1734520183776" duration="15167000" />
+      <workItem from="1734520183776" duration="15312000" />
+      <workItem from="1734600114757" duration="1143000" />
     </task>
     <task id="LOCAL-00014" summary="Functioning dashboard for simulations&#10;fixed bug in committing transactions to sqlite">
       <created>1582368099002</created>
@@ -879,7 +886,7 @@
       <option name="project" value="LOCAL" />
       <updated>1615727183521</updated>
     </task>
-    <option name="localTasksCounter" value="65" />
+    <option name="localTasksCounter" value="66" />
     <servers />
   </component>
   <component name="TypeScriptGeneratedFilesManager">
@@ -911,7 +918,6 @@
     </option>
   </component>
   <component name="VcsManagerConfiguration">
-    <MESSAGE value="Switched map drawing to altair for performance reasons.&#10;&#10;Added panel with simulation metadata." />
     <MESSAGE value="Further improvements on Altair visualizations" />
     <MESSAGE value="Added encoded favicon in the code." />
     <MESSAGE value="Fixed multiple minor bugs and updated documentation" />
@@ -936,7 +942,8 @@
     <MESSAGE value="bumped up minor version" />
     <MESSAGE value="fixed many bugs and started migrating to pyproject.toml" />
     <MESSAGE value="fixed many bugs" />
-    <option name="LAST_COMMIT_MESSAGE" value="fixed many bugs" />
+    <MESSAGE value="updated the READme" />
+    <option name="LAST_COMMIT_MESSAGE" value="updated the READme" />
   </component>
   <component name="XDebuggerManager">
     <watches-manager>
diff --git a/condarecipe/epigrass/meta.yaml b/condarecipe/epigrass/meta.yaml
deleted file mode 100644
index 647ecf3..0000000
--- a/condarecipe/epigrass/meta.yaml
+++ /dev/null
@@ -1,88 +0,0 @@
-{% set name = "epigrass" %}
-{% set version = "3.0.3" %}
-
-package:
-  name: "{{ name|lower }}"
-  version: "{{ version }}"
-
-source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7d98ca1441a4ef3f2eaf6d2c8a7919bde9c6ce488259e02e9f1f9218b07e5111
-
-build:
-  number: 0
-  entry_points:
-    - epirunner = Epigrass.manager:main
-  script: "{{ PYTHON }} -m pip install . -vv"
-
-requirements:
-  host:
-    - altair
-    - cython
-    - datashader
-    - dbfread
-    - epimodels
-    - fiona
-    - geopandas
-    - geoviews
-    - holoviews
-    - matplotlib
-    - networkx
-    - numpy
-    - pandas
-    - panel
-    - pip
-    - pweave
-    - pymysql
-    - python
-    - redis
-    - scikit-image
-    - shapely
-    - sqlalchemy
-    - sqlobject
-    - tqdm
-    - redis-py
-  run:
-    - altair
-    - cython
-    - datashader
-    - dbfread
-    - epimodels
-    - fiona
-    - geopandas
-    - geoviews
-    - holoviews
-    - matplotlib
-    - networkx
-    - numpy
-    - pandas
-    - panel
-    - pweave
-    - pymysql
-    - python
-    - redis
-    - scikit-image
-    - shapely
-    - sqlalchemy
-    - sqlobject
-    - tqdm
-    - redis-py
-
-test:
-  imports:
-    - Epigrass
-  commands:
-    - epirunner --help
-
-about:
-  home: "http://epigrass.sourceforge.net"
-  license: GPL
-  license_family: GPL
-  license_file: 
-  summary: "Epidemiological Geo-Referenced Analysis and Simulation System"
-  doc_url: 
-  dev_url: 
-
-extra:
-  recipe-maintainers:
-    - fccoelho
diff --git a/pyproject.toml b/pyproject.toml
index a3ae1fa..4b8d4df 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,6 +9,17 @@ description = "Epidemiological Geo-Referenced Analysis and Simulation System"
 readme = "README.md"
 license = {text="GPLv3"}
 requires-python = ">=3.12"
+classifiers = [
+    "License :: OSI Approved :: GPLv3 License",
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: researchers",
+    "Natural Language :: English",
+    "Topic :: Scientific/Epidemiology",
+]
 dependencies = [
     "altair>=5.5.0",
     "cython>=3.0.11",
@@ -35,6 +46,13 @@ dependencies = [
     "tqdm>=4.67.1",
 ]
 
+[project.urls]
+Homepage = "https://epigrass.readthedocs.io"
+Source = "https://github.com/fccoelho/epigrass"
+
+[tool.setuptools]
+packages = ["Epigrass"]
+
 [tool.uv]
 package = true
 
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 861a9f5..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,5 +0,0 @@
-[egg_info]
-tag_build = 
-tag_date = 0
-tag_svn_revision = 0
-
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 42b4a37..0000000
--- a/setup.py
+++ /dev/null
@@ -1,34 +0,0 @@
-from setuptools import setup
-# from Cython.Build import cythonize
-from Epigrass.__version__ import version
-
-with open('requirements.txt') as f:
-    reqs = [p.strip() for p in f.readlines()]
-
-setup(name='epigrass',
-      version=version,
-      author='Flavio Codeco Coelho, Claudia Torres Codeco',
-      author_email='fccoelho@gmail.com',
-      maintainer='Flavio Codeco Coelho',
-      maintainer_email='fccoelho@gmail.com',
-      url='http://epigrass.sourceforge.net',
-      description='Epidemiological Geo-Referenced Analysis and Simulation System',
-      long_description='EpiGrass is a simulator of epidemics over networks.  Its is a scientific tool created for simulations and scenario analysis in Network epidemiology.',
-      download_url='http://sourceforge.net/project/showfiles.php?group_id=128000',
-      license='GPL',
-      packages=['Epigrass'],
-      setup_requires=['cython'],
-      install_requires=reqs,
-      entry_points={
-          'console_scripts': [
-              'epirunner = Epigrass.manager:main',
-          ],
-      },
-      # ext_modules=cythonize('Epigrass/models.py'),
-      zip_safe=False,
-      include_package_data=True,
-      package_data={'': ['COPYING', 'epigrass.desktop', '*.rst', '*.tex', '*.png', '*.jpg']},
-      data_files=[('/usr/share/pixmaps', ['egicon.png']),
-                  ('/usr/share/doc/epigrass/', ['docs/build/latex/Epigrass.pdf']),
-                  ('/usr/share/applications', ['epigrass.desktop'])]
-      )