Last minute fixes, tests went through

Slight changes to the README, added a Misc section.
A last check / modification of docstrings.

Author: fsoubelet

README.md

@@ -1,6 +1,6 @@
 # PyhDToolkit: An all-in-one toolkit package for Python work in my PhD.
 
-This repository is a package gathering a number of Python utilities for my PhD.
+This repository is a package gathering a number of Python utilities for my work.
 
 ## Installation
 
@@ -35,7 +35,7 @@ make tests
 
 ## Standards, Tools and VCS
 
-This repository respects the PyCharm docstring format (because it's the tool I use), and uses [Black][black_formatter] as a code formatter.
+This repository respects the PyCharm docstring format, and uses [Black][black_formatter] as a code formatter.
 The default enforced line length is 120 characters.
 You can lint the code with:
 ```bash
@@ -45,11 +45,28 @@ make black
 VCS is done through [git][git_ref] and follows the [Gitflow][gitflow_ref] workflow.
 As a consequence, make sure to always install from `master`.
 
+## Miscellaneous Goodies
+
+Feel free to explore the `Makefile` and make use of the functions it offers.
+You can get an idea of what is available to you by running:
+```bash
+make help
+```
+
+This repository currently comes with an `environment.yml` file to reproduce a fully compatible conda environment.
+You can install this environment and add it to your ipython kernel by running:
+```bash
+make condaenv
+```
+
+A Dockerfile and later on an [OCI][oci_ref]-compliant file are to come.
+
 ## License
 
-Copyright © 2019 Felix Soubelet. [MIT License][license]
+Copyright © 2019-2020 Felix Soubelet. [MIT License][license]
 
 [black_formatter]: https://github.com/psf/black
 [gitflow_ref]: https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow
 [git_ref]: https://git-scm.com/
-[license]: https://github.com/fsoubelet/PyhDToolkit/blob/master/LICENSE
+[license]: https://github.com/fsoubelet/PyhDToolkit/blob/master/LICENSE
+[oci_ref]: https://www.opencontainers.org/

pyhdtoolkit/cpymadtools/latwiss.py

@@ -53,12 +53,11 @@ def plot_latwiss(cpymad_instance, title: str, fig_size: tuple, ncells: int, **kw
         Provided with an active Cpymad class after having ran a script, will create a plot representing nicely the
         lattice layout and the beta functions along with the horizontal dispertion function. Original code is from
         Guido Sterbini.
-        :param cpymad_instance: an instanciated `cpymad.MadX` object.
+        :param cpymad_instance: an instanciated `cpymad.madx.Madx` object.
         :param title: title of your plot.
         :param fig_size: figure size.
         :param ncells: number of cells of your lattice.
-        :param kwargs:
-        :return:
+        :return: nothing, plots and eventually saves the figure as a file.
         """
         # Getting kwargs and instantiating
         x_limits = kwargs.get("xlim", None)
@@ -129,10 +128,9 @@ def plot_machine_survey(cpymad_instance, fig_size: tuple, **kwargs) -> None:
         """
         Provided with an active Cpymad class after having ran a script, will create a plot representing the machine
         geometry in 2D. Original code is from Guido Sterbini.
-        :param cpymad_instance: an instanciated `cpymad.MadX` object.
+        :param cpymad_instance: an instanciated `cpymad.madx.Madx` object.
         :param fig_size: figure size.
-        :param kwargs:
-        :return:
+        :return: nothing, plots and eventually saves the figure as a file.
         """
         savefig = kwargs.get("savefig", False)
         cpymad_instance.input("survey;")

pyhdtoolkit/cpymadtools/plotters.py

@@ -58,7 +58,7 @@ def plot_normalized_phase_space(cpymad_instance, u_coordinates, pu_coordinates,
         """
         Plots the normalized phase space of a particle distribution when provided by position and momentum coordinates
         for a specific plane.
-        :param cpymad_instance: an instanciated `cpymad.MadX` object.
+        :param cpymad_instance: an instanciated `cpymad.madx.Madx` object.
         :param u_coordinates: coordinates of particles.
         :param pu_coordinates: momentum coordinates of particles.
         :param kwargs: The looked for keywords are `size`, `plane`, and `savefig`. They give the possibility of
@@ -104,7 +104,7 @@ def plot_normalized_phase_space_colored(cpymad_instance, u_coordinates, pu_coord
         Plots the normalized phase space of a particle distribution when provided by position and momentum coordinates
         for a specific plane. Each particle trajectory has its own color on the plot, within the limit of pyplot's 156
         named colors. The sequence repeats after the 156th color.
-        :param cpymad_instance: an instanciated `cpymad.MadX` object.
+        :param cpymad_instance: an instanciated `cpymad.madx.Madx` object.
         :param u_coordinates: coordinates of particles.
         :param pu_coordinates: momentum coordinates of particles.
         :param kwargs: The looked for keywords are `size`, `plane`, and `savefig`. They give the possibility of
@@ -160,7 +160,7 @@ def farey_sequence(n: int) -> list:
         """
         Return the n-th farey_sequence sequence, ascending. Original code from Rogelio Tomás.
         :param n: the order up to which we want to calculate the sequence.
-        :return: the sequence.
+        :return: the sequence as a list.
         """
         seq = [[0, 1]]
         a, b, c, d = 0, 1, 1, n
@@ -215,7 +215,7 @@ def plot_tune_diagram(
     ) -> None:
         """
         Plots the evolution of particles' tunes on a Tune Diagram.
-        :param cpymad_instance: an instanciated `cpymad.MadX` object.
+        :param cpymad_instance: an instanciated `cpymad.madx.Madx` object.
         :param v_qx: values of the horizontal tune Qx. Can be only one value.
         :param vxgood:
         :param v_qy: values of the vertical tune Qy. Can be only one value.

pyhdtoolkit/studies/triplet_errors/algo.py

@@ -28,8 +28,8 @@ class GridCompute:
     """
     Algorithm as a class to run the simulations and analyze the outputs.
 
-    Will prompt error values for confirmation, run MAD-X simulations through a `Cpymad.Madx` object, get beta-beating
-    values from the outputs and return the appropriate structures.
+    Will prompt error values for confirmation, run MAD-X simulations through a `cpymad.madx.Madx` object,
+    get beta-beating values from the outputs and return the appropriate structures.
     """
 
     def __init__(self):