update README and some paths

sissaschool · Nov 14, 2019 · 59a5189 · 59a5189
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diff --git a/README.md b/README.md
@@ -32,25 +32,25 @@ See the [`examples/example_commandline_NaCl`](examples/example_commandline_NaCl/
  - 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.
-  You can simply pip-install thermocepstrum with `pip install thermocepstrum`.
+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.
 
   Alternatively:
+
   1. Clone this repository: `git clone https://github.com/lorisercole/thermocepstrum.git`
-  2. Install the package with pip (dependencies will be automatically downloaded). For example:
-```
-cd thermocepstrum
-pip install .
-```
-  or
-```
-cd thermocepstrum_gui
-pip install .
-```
-  or, if you are on a unix system, simply run `setup.sh`
-  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).
+  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.
+
+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).
 
 ### 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/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('..')\n",
+    "    path.append('../thermocepstrum')\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('..')\n",
+    "    path.append('../thermocepstrum')\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/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r`
+`../../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`
 
 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/analysis.py ../data/NaCl.dat -k flux -j 'vcm[1]' -t 5.0 -V 65013.301261 -w 0.1 --FSTAR 14.0 -r
+#../../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