Rewrite GUI branch with reorganize_package branch

The original package folder organization has been restored.
sissaschool · Nov 15, 2019 · e806de9 · e806de9
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -12,8 +12,9 @@ Here are a few guidelines to consider when contributing.
 - When you are done with a branch and want to **merge** it to `develop`, submit a *Pull request*. Unless it is a simple fix, and especially if it is a new functionality, this will help to keep the code clean and find potential bugs beforehand. Also, it will help to standardize the style.
 - Before updating the `develop` branch, make **tests**!
 - Try to make **commits** as specific as possible, and document the changes.
-- note that some files are copied inside the source tree by the script copy_readmes_in_packages.sh (it is not possible to use symbolic links to build the python package)
-- this repository has two python packages inside it: **thermocepstrum**, the full library and the command line interface, that is compatible with python 2.7 and 3.x, and **thermocepstrum_gui**, that contains the GUI only, it depends on **thermocepstrum** and it is NOT python 2.7 compatible.
+- This repository contains two python packages:
+    - **thermocepstrum**, the full library and the command line interface, that is compatible with Python 2.7 and 3.x.
+    - **thermocepstrum_gui**, that contains the GUI only, it depends on **thermocepstrum** and it is *NOT* Python 2.7 compatible.
 
 
 ## WISH LIST

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,11 +1,10 @@
 recursive-include examples *
-include thermocepstrum/utils/plot_style.mplstyle
-include thermocepstrum/setup.json
-include thermocepstrum_gui/assets/icon.gif
-include thermocepstrum_gui/assets/languages.json
 include LICENSE.txt
 include thermocepstrum/README.md
-include thermocepstrum/README_GUI.md
+include thermocepstrum/metadata.json
+include thermocepstrum/utils/plot_style.mplstyle
 exclude thermocepstrum/utils/blocks.py
 exclude thermocepstrum/utils/blockanalysis.py
-prune thermocepstrum/old_src
+include thermocepstrum_gui/README_GUI.md
+include thermocepstrum_gui/assets/icon.gif
+include thermocepstrum_gui/assets/languages.json
diff --git a/README.md b/README.md
@@ -19,38 +19,32 @@ See the [`examples/example_commandline_NaCl`](examples/example_commandline_NaCl/
 ### Requirements
 #### only cepstral analysis (command line interface)
  - Python 2.7 or 3.x
- - Numpy
- - Scipy
- - Matplotlib
+ - numpy
+ - ncipy
+ - matplotlib
 #### graphical user interface
  - all the requirements of cepstral analysis
- - python 3 only
+ - Python 3 only
  - tkinter
  - future-fstrings
- - pillow (you may need to run `pip install pillow --upgrade` )
+ - pillow (you may need upgrade it)
  - tk-html-widgets
  - markdown2
 
 ### Installation
-We provide two python packages. The core library and the command line interface are in the subdirectory `thermocepstrum`, while the GUI is in the `thermocepstrum_gui` subdirectory. Remember that the GUI requires python 3, while the library and the command line interface don't. That's why we have two packages.
-  You can simply pip-install thermocepstrum with `pip install thermocepstrum` from the pypi repository.
-
+  You can simply pip-install thermocepstrum downloading it from PyPI with `pip install thermocepstrum`.
+
   Alternatively:
 
   1. Clone this repository: `git clone https://github.com/lorisercole/thermocepstrum.git`
-  2. cd into the new directory created by git
-   * system where `setup.sh` does work:
-     1. run the bash script `setup.sh` and you are done (skip next steps).
-   * system where `setup.sh` does not work:
-     1. copy the files `README.md README_GUI.md LICENSE.txt` in the source folders `thermocepstrum/thermocepstrum` and `thermocepstrum_gui/thermocepstrum_gui/`
-     2. `cd thermocepstrum; pip install .`
-     3. `cd thermocepstrum_gui; pip install`
-
-The copy is needed  because during python packaging it is not possible to include files from parent directories, and we want to have only a single version of the READMEs in the project tree.
+  2. Install the package with pip (dependencies will be automatically downloaded). For example:
+```
+cd thermocepstrum
+pip install .
+```
+  You are done! You can check that the installation is working by trying to run the command `thermocepstrum-analysis`.
 
-You are done! You can check that the installation is working by trying to run the command `thermocepstrum-analysis`.
-The graphical user interface is started with the command `thermocepstrum-gui` (only if you installed it).
+  If you use Python 3, the Graphical User Interface will be installed and can be started with the command `thermocepstrum-gui`.
 
 ### Issues
-You are strongly encouraged to report any issue on the [official](https://github.com/lorisercole/thermocepstrum/issues) GitHub issues page.
-
+  You are strongly encouraged to report any issue on the [official](https://github.com/lorisercole/thermocepstrum/issues) GitHub issues page.
diff --git a/copy_readmes_in_packages.sh b/copy_readmes_in_packages.sh
diff --git a/examples/example_cepstrum_doublecomp_NaCl.ipynb b/examples/example_cepstrum_doublecomp_NaCl.ipynb
@@ -21,7 +21,7 @@
     "    import thermocepstrum as tc\n",
     "except ImportError:\n",
     "    from sys import path\n",
-    "    path.append('../thermocepstrum')\n",
+    "    path.append('..')\n",
     "    import thermocepstrum as tc\n",
     "\n",
     "c = plt.rcParams['axes.prop_cycle'].by_key()['color']"

diff --git a/examples/example_cepstrum_singlecomp_silica.ipynb b/examples/example_cepstrum_singlecomp_silica.ipynb
@@ -21,7 +21,7 @@
     "    import thermocepstrum as tc\n",
     "except ImportError:\n",
     "    from sys import path\n",
-    "    path.append('../thermocepstrum')\n",
+    "    path.append('..')\n",
     "    import thermocepstrum as tc\n",
     "\n",
     "c = plt.rcParams['axes.prop_cycle'].by_key()['color']"

diff --git a/examples/example_commandline_NaCl/README.md b/examples/example_commandline_NaCl/README.md
@@ -7,7 +7,7 @@ Symply run, after installing the package, the following command (see `command.sh
 thermocepstrum-analysis ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
 ```
 If the package is not installed you can run this instead:
-`../../thermocepstrum/thermocepstrum/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r`
+`../../thermocepstrum/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r`
 
 The options have the following meaning:
 * `-k flux` use the columns with header `flux` as the energy flux

diff --git a/examples/example_commandline_NaCl/command.sh b/examples/example_commandline_NaCl/command.sh
@@ -4,4 +4,4 @@
 thermocepstrum-analysis ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
 
 # if thermocepstrum is not pip installed use:
-#../../thermocepstrum/thermocepstrum/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
+#../../thermocepstrum/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
diff --git a/thermocepstrum/thermocepstrum/setup.json → setup.json b/thermocepstrum/thermocepstrum/setup.json → setup.json
@@ -42,11 +42,11 @@
     },
     "entry_points": {
         "console_scripts": [
-            "thermocepstrum-analysis = thermocepstrum.analysis:main"
+            "thermocepstrum-analysis=thermocepstrum.analysis:main"
         ]
     },
+    "gui_version" : "0.0.2a",
     "dev_state" : "alpha",
     "release_date" : "NOT REL.",
     "credits" : "developed at SISSA, Via Bonomea, 265 - 34136 Trieste ITALY"
-
 }
diff --git a/setup.py b/setup.py
@@ -0,0 +1,50 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+from setuptools import setup, find_packages
+from os import path
+import sys
+import json
+
+GUI_dependencies = [
+        "future-fstrings",
+        "markdown2",
+        "pillow>=5.4.0",
+        "tk-html-widgets",
+        "uncertainties"
+]
+
+if sys.version_info[0] == 2:
+    INSTALL_GUI = False
+    sys.stderr.write("************* GUI does not support Python 2: it will not be installed. That's a pity! *************")
+elif sys.version_info[0] == 3:
+    INSTALL_GUI = True
+
+
+if __name__ == '__main__':
+    THIS_FOLDER = path.split(path.abspath(__file__))[0]
+
+    with open(path.join(THIS_FOLDER, 'README.md'), 'r') as fh:
+        long_description = fh.read()
+
+    with open(path.join(THIS_FOLDER, 'setup.json'), 'r') as info:
+        SETUP_JSON = json.load(info)
+
+    if INSTALL_GUI:
+        exclude_packages = []
+        SETUP_JSON['install_requires'] += GUI_dependencies
+        SETUP_JSON['entry_points']['console_scripts'] += ["thermocepstrum-gui = thermocepstrum_gui.main:run"]
+        with open(path.join(THIS_FOLDER, 'thermocepstrum/metadata.json'), 'w') as fh:
+           json.dump(SETUP_JSON, fh)
+    else:
+        exclude_packages = ['thermocepstrum_gui*']
+
+    setup(include_package_data=True,
+          packages=find_packages(exclude=exclude_packages),
+          long_description=long_description,
+          long_description_content_type='text/markdown',
+#          setup_requires=['reentry'],
+          **SETUP_JSON)
+
+# https://packaging.python.org/guides/distributing-packages-using-setuptools/#setup-args
+# https://setuptools.readthedocs.io/en/latest/setuptools.html#including-data-files
diff --git a/setup.sh b/setup.sh
diff --git a/thermocepstrum/tests/README.md → tests/README.md b/thermocepstrum/tests/README.md → tests/README.md
diff --git a/tests/data b/tests/data
@@ -0,0 +1 @@
+../examples/data
diff --git a/thermocepstrum/tests/test_as_example.py → tests/test_as_example.py b/thermocepstrum/tests/test_as_example.py → tests/test_as_example.py
diff --git a/thermocepstrum/MANIFEST.in b/thermocepstrum/MANIFEST.in
diff --git a/thermocepstrum/README.md b/thermocepstrum/README.md
@@ -0,0 +1 @@
+../README.md
diff --git a/thermocepstrum/thermocepstrum/__init__.py → thermocepstrum/__init__.py b/thermocepstrum/thermocepstrum/__init__.py → thermocepstrum/__init__.py
diff --git a/thermocepstrum/thermocepstrum/analysis.py → thermocepstrum/analysis.py b/thermocepstrum/thermocepstrum/analysis.py → thermocepstrum/analysis.py
diff --git a/thermocepstrum/thermocepstrum/heatcurrent.py → thermocepstrum/heatcurrent.py b/thermocepstrum/thermocepstrum/heatcurrent.py → thermocepstrum/heatcurrent.py
diff --git a/...mocepstrum/thermocepstrum/i_o/__init__.py → thermocepstrum/i_o/__init__.py b/...mocepstrum/thermocepstrum/i_o/__init__.py → thermocepstrum/i_o/__init__.py
diff --git a/...ermocepstrum/i_o/extract_lammps_thermo.sh → thermocepstrum/i_o/extract_lammps_thermo.sh b/...ermocepstrum/i_o/extract_lammps_thermo.sh → thermocepstrum/i_o/extract_lammps_thermo.sh
diff --git a/...hermocepstrum/i_o/read_lammps_datafile.py → thermocepstrum/i_o/read_lammps_datafile.py b/...hermocepstrum/i_o/read_lammps_datafile.py → thermocepstrum/i_o/read_lammps_datafile.py
diff --git a/...um/thermocepstrum/i_o/read_lammps_dump.py → thermocepstrum/i_o/read_lammps_dump.py b/...um/thermocepstrum/i_o/read_lammps_dump.py → thermocepstrum/i_o/read_lammps_dump.py
diff --git a/...rum/thermocepstrum/i_o/read_lammps_log.py → thermocepstrum/i_o/read_lammps_log.py b/...rum/thermocepstrum/i_o/read_lammps_log.py → thermocepstrum/i_o/read_lammps_log.py
diff --git a/...trum/thermocepstrum/i_o/read_tablefile.py → thermocepstrum/i_o/read_tablefile.py b/...trum/thermocepstrum/i_o/read_tablefile.py → thermocepstrum/i_o/read_tablefile.py
diff --git a/thermocepstrum/thermocepstrum/md/__init__.py → thermocepstrum/md/__init__.py b/thermocepstrum/thermocepstrum/md/__init__.py → thermocepstrum/md/__init__.py
diff --git a/thermocepstrum/thermocepstrum/md/acf.py → thermocepstrum/md/acf.py b/thermocepstrum/thermocepstrum/md/acf.py → thermocepstrum/md/acf.py
diff --git a/thermocepstrum/thermocepstrum/md/aic.py → thermocepstrum/md/aic.py b/thermocepstrum/thermocepstrum/md/aic.py → thermocepstrum/md/aic.py
diff --git a/thermocepstrum/thermocepstrum/md/armodel.py → thermocepstrum/md/armodel.py b/thermocepstrum/thermocepstrum/md/armodel.py → thermocepstrum/md/armodel.py
diff --git a/thermocepstrum/thermocepstrum/md/cepstral.py → thermocepstrum/md/cepstral.py b/thermocepstrum/thermocepstrum/md/cepstral.py → thermocepstrum/md/cepstral.py
diff --git a/thermocepstrum/thermocepstrum/md/lpfilter.py → thermocepstrum/md/lpfilter.py b/thermocepstrum/thermocepstrum/md/lpfilter.py → thermocepstrum/md/lpfilter.py
diff --git a/thermocepstrum/thermocepstrum/md/mdsample.py → thermocepstrum/md/mdsample.py b/thermocepstrum/thermocepstrum/md/mdsample.py → thermocepstrum/md/mdsample.py
diff --git a/thermocepstrum/thermocepstrum/md/tools.py → thermocepstrum/md/tools.py b/thermocepstrum/thermocepstrum/md/tools.py → thermocepstrum/md/tools.py
diff --git a/thermocepstrum/thermocepstrum/md/units.py → thermocepstrum/md/units.py b/thermocepstrum/thermocepstrum/md/units.py → thermocepstrum/md/units.py
diff --git a/thermocepstrum/setup.py b/thermocepstrum/setup.py
diff --git a/thermocepstrum/tests/data b/thermocepstrum/tests/data
diff --git a/thermocepstrum/thermocepstrum/MANIFEST.in b/thermocepstrum/thermocepstrum/MANIFEST.in
diff --git a/...cepstrum/thermocepstrum/utils/__init__.py → thermocepstrum/utils/__init__.py b/...cepstrum/thermocepstrum/utils/__init__.py → thermocepstrum/utils/__init__.py
diff --git a/...rum/thermocepstrum/utils/blockanalysis.py → thermocepstrum/utils/blockanalysis.py b/...rum/thermocepstrum/utils/blockanalysis.py → thermocepstrum/utils/blockanalysis.py
diff --git a/...mocepstrum/thermocepstrum/utils/blocks.py → thermocepstrum/utils/blocks.py b/...mocepstrum/thermocepstrum/utils/blocks.py → thermocepstrum/utils/blocks.py
diff --git a/...trum/thermocepstrum/utils/loadAfterPlt.py → thermocepstrum/utils/loadAfterPlt.py b/...trum/thermocepstrum/utils/loadAfterPlt.py → thermocepstrum/utils/loadAfterPlt.py
diff --git a/.../thermocepstrum/utils/plot_style.mplstyle → thermocepstrum/utils/plot_style.mplstyle b/.../thermocepstrum/utils/plot_style.mplstyle → thermocepstrum/utils/plot_style.mplstyle
diff --git a/thermocepstrum/thermocepstrum/utils/utils.py → thermocepstrum/utils/utils.py b/thermocepstrum/thermocepstrum/utils/utils.py → thermocepstrum/utils/utils.py
diff --git a/thermocepstrum_gui/MANIFEST.in b/thermocepstrum_gui/MANIFEST.in
diff --git a/thermocepstrum_gui/README_GUI.md b/thermocepstrum_gui/README_GUI.md
@@ -0,0 +1 @@
+../README_GUI.md
diff --git a/...pstrum_gui/thermocepstrum_gui/__init__.py → thermocepstrum_gui/__init__.py b/...pstrum_gui/thermocepstrum_gui/__init__.py → thermocepstrum_gui/__init__.py
diff --git a/...gui/thermocepstrum_gui/assets/__init__.py → thermocepstrum_gui/assets/__init__.py b/...gui/thermocepstrum_gui/assets/__init__.py → thermocepstrum_gui/assets/__init__.py
@@ -2,16 +2,13 @@
 from pkg_resources import resource_stream, resource_string
 import json
 
-with resource_stream('thermocepstrum_gui', 'setup.json') as JS:
+with resource_stream('thermocepstrum', 'metadata.json') as JS:
     METADATA = json.load(JS)
 
-with resource_stream('thermocepstrum', 'setup.json') as JS:
-    METADATAtc = json.load(JS)
-
 with resource_stream(__name__, 'languages.json') as JS:
     LANGUAGES = json.load(JS)
 
 ICON = resource_string(__name__, 'icon.gif')
 
-README_MD = resource_string('thermocepstrum_gui', 'README.md')
+README_MD = resource_string('thermocepstrum', 'README.md')
 README_GUI_MD = resource_string('thermocepstrum_gui', 'README_GUI.md')
diff --git a/...um_gui/thermocepstrum_gui/assets/icon.gif → thermocepstrum_gui/assets/icon.gif b/...um_gui/thermocepstrum_gui/assets/icon.gif → thermocepstrum_gui/assets/icon.gif
diff --git a/.../thermocepstrum_gui/assets/languages.json → thermocepstrum_gui/assets/languages.json b/.../thermocepstrum_gui/assets/languages.json → thermocepstrum_gui/assets/languages.json
diff --git a/...thermocepstrum_gui/assets/window_icon.ico → thermocepstrum_gui/assets/window_icon.ico b/...thermocepstrum_gui/assets/window_icon.ico → thermocepstrum_gui/assets/window_icon.ico
diff --git a/...m_gui/thermocepstrum_gui/core/__init__.py → thermocepstrum_gui/core/__init__.py b/...m_gui/thermocepstrum_gui/core/__init__.py → thermocepstrum_gui/core/__init__.py
diff --git a/...i/thermocepstrum_gui/core/control_unit.py → thermocepstrum_gui/core/control_unit.py b/...i/thermocepstrum_gui/core/control_unit.py → thermocepstrum_gui/core/control_unit.py
diff --git a/...m_gui/thermocepstrum_gui/core/settings.py → thermocepstrum_gui/core/settings.py b/...m_gui/thermocepstrum_gui/core/settings.py → thermocepstrum_gui/core/settings.py
diff --git a/...thermocepstrum_gui/interfaces/__init__.py → thermocepstrum_gui/interfaces/__init__.py b/...thermocepstrum_gui/interfaces/__init__.py → thermocepstrum_gui/interfaces/__init__.py
diff --git a/...rmocepstrum_gui/interfaces/fileManager.py → thermocepstrum_gui/interfaces/fileManager.py b/...rmocepstrum_gui/interfaces/fileManager.py → thermocepstrum_gui/interfaces/fileManager.py
diff --git a/...ocepstrum_gui/interfaces/fstarSelector.py → ...ocepstrum_gui/interfaces/fstarSelector.py b/...ocepstrum_gui/interfaces/fstarSelector.py → ...ocepstrum_gui/interfaces/fstarSelector.py
diff --git a/...cepstrum_gui/interfaces/headerSelector.py → ...cepstrum_gui/interfaces/headerSelector.py b/...cepstrum_gui/interfaces/headerSelector.py → ...cepstrum_gui/interfaces/headerSelector.py
diff --git a/...cepstrum_gui/interfaces/otherVariables.py → ...cepstrum_gui/interfaces/otherVariables.py b/...cepstrum_gui/interfaces/otherVariables.py → ...cepstrum_gui/interfaces/otherVariables.py
diff --git a/...ocepstrum_gui/interfaces/pstarSelector.py → ...ocepstrum_gui/interfaces/pstarSelector.py b/...ocepstrum_gui/interfaces/pstarSelector.py → ...ocepstrum_gui/interfaces/pstarSelector.py
diff --git a/...mocepstrum_gui/thermocepstrum_gui/main.py → thermocepstrum_gui/main.py b/...mocepstrum_gui/thermocepstrum_gui/main.py → thermocepstrum_gui/main.py
@@ -19,7 +19,7 @@
 
 from thermocepstrum_gui.interfaces import *
 from thermocepstrum_gui.utils.custom_widgets import *
-from thermocepstrum_gui.assets import ICON, METADATA, METADATAtc, LANGUAGES
+from thermocepstrum_gui.assets import ICON, METADATA, LANGUAGES
 # Verify that thermocepstrum is installed
 try:
     import thermocepstrum
@@ -120,11 +120,11 @@ def show_software_info(self):
         """
         print('------------------- Thermocepstrum GUI -------------------')
         print('')
-        print('\t\t\tGUI version: {}'.format(METADATA['version']))
-        print('\t\t\tThermocepstrum version: {}'.format(METADATAtc['version']))
+        print('\t\t\tGUI version: {}'.format(METADATA['gui_version']))
+        print('\t\t\tThermocepstrum version: {}'.format(METADATA['version']))
         print('\t\t\tDev state: {}'.format(METADATA['dev_state']))
         print('\t\t\tLast release: {}'.format(METADATA['release_date']))
-        print('\t\t\tDevelopers: {}'.format(METADATAtc['author']))
+        print('\t\t\tDevelopers: {}'.format(METADATA['author']))
         print('\t\t\tURL: {}'.format(METADATA['url']))
         print('')
         print('This software is an open-source project licensed under {}'.format(METADATA['license']))

diff --git a/thermocepstrum_gui/setup.py b/thermocepstrum_gui/setup.py
diff --git a/...ocepstrum_gui/thermocepstrum_gui/thcp.ini → thermocepstrum_gui/thcp.ini b/...ocepstrum_gui/thermocepstrum_gui/thcp.ini → thermocepstrum_gui/thcp.ini
diff --git a/thermocepstrum_gui/thermocepstrum_gui/MANIFEST.in b/thermocepstrum_gui/thermocepstrum_gui/MANIFEST.in
diff --git a/thermocepstrum_gui/thermocepstrum_gui/setup.json b/thermocepstrum_gui/thermocepstrum_gui/setup.json
diff --git a/...rum_gui/thermocepstrum_gui/utils/Graph.py → thermocepstrum_gui/utils/Graph.py b/...rum_gui/thermocepstrum_gui/utils/Graph.py → thermocepstrum_gui/utils/Graph.py
diff --git a/..._gui/thermocepstrum_gui/utils/__init__.py → thermocepstrum_gui/utils/__init__.py b/..._gui/thermocepstrum_gui/utils/__init__.py → thermocepstrum_gui/utils/__init__.py