Improve slightly the examples of LumiWorks. Also fix typos. (#304)

* Insert one sentence to explain why conda install --file ./requirements-optional.txt is suggested.

* More explanations in the README.rst .

* Fix typos. Specify how to get a PMG_MAPI_KEY.

* Several minor modifs

* Minor modif, slightly more accurate wording.

* Transfer the section explaining how to install conda from the abitutorial/README.md file.

* Improve the previous commit

* And now ...

* Next trial

* Now should work

* Complete README.rst with information coming from abitutorials. Also import the manager directory from abitutorials.

* Fix formatting problems.

* More formatting fixes.

* Continue to work on the README.rst, minor modifs.

* Fix links

* Commas

* Minor correction

* Previous modif did not work

* Fixes

* Unify the environment name, now abienv everywhere (instead of possibly abipy3.6).

* Final modifs of README.rst

* Fix missing :: in README.rst , causing unformatted apprearance on github.

* Remove the managers dir, and update the associated doc.

* Write explicitly Setyawan and Curtarolo 2010

* Improve slightly the examples of LumiWorks. Also fix a typo.

---------

Co-authored-by: trunk <trunk@abinit.org>

abipy/examples/flows/run_gs_vs_kpts.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 r"""
-Convergence studiy with different k-meshes
+Convergence study with different k-meshes
 ==========================================
 
 In this example,

abipy/examples/flows/run_lumi_Eu_doped_SLA.py

@@ -1,22 +1,22 @@
 #!/usr/bin/env python
 r"""
-Delta SCF constrained occupation method calculation, to determine luminescent properties.
-=========================================================================================
+Delta SCF calculation: luminescence of an Eu-doped phosphor
+===========================================================
 
-This example shows how to compute the luminescent properties of Eu doped phosphor.
-It uses a 36 atoms cell of SrLiAl3N4. Two non-equivalent Sr sites are availabe for Eu, resulting
+This example shows how to compute the luminescent properties of an Eu-doped phosphor.
+It uses a 36 atoms cell of SrLiAl3N4. Two non-equivalent Sr sites are available for Eu, resulting
 in two independent LumiWork. The creation of the supercells is done with make_doped_supercell().
 
 Steps, for each structure:
-1) Relaxation in the ground state
-2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time
+1) Relaxation in the ground state.
+2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time.
 3) Scf computation in the relaxed/unrelaxed ground/excited state (4 computations).
 
 Even if we use minimal settings, the workflow takes around one hour to run on one core.
-Filepaths of the 6 runs are stored in outdata/lumi.json of each work
-A quick post-processing is automatically done at the end of a LumiWork
+Filepaths of the 6 runs are stored in outdata/lumi.json of each work.
+A quick post-processing is automatically done at the end of a LumiWork,
 and stored in outdata/Delta_SCF.json of each work, with relevant luminescent properties
-(ZPL energy, Stoke Shift, \Delta Q,...), see abipy/lumi/delta_scf.py
+(ZPL energy, Stoke Shift, \Delta Q,...), see abipy/lumi/delta_scf.py .
 """
 
 import sys

abipy/examples/flows/run_lumi_NV_center.py

@@ -1,15 +1,15 @@
 #!/usr/bin/env python
 r"""
-Delta SCF constrained occupation method calculation, to determine luminescent properties.
+Delta SCF calculation: luminescence of the NV- center in diamond.
 =========================================================================================
 
 This example shows how to compute the luminescent properties of the NV- center in diamond.
-It uses a 64 atoms supercell, where one C atom was replaced by one N atom and one vacancy was created.
+It uses a 64-atom supercell, where one C atom was replaced by one N atom and one vacancy was created.
 See Fig.3 of https://doi.org/10.1103/PhysRevB.104.045303 for the setting of electron occupation
 in the ground/excited state.
 Steps:
-1) Relaxation in the ground state
-2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time
+1) Relaxation in the ground state.
+2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time.
 3) Scf computation in the relaxed/unrelaxed ground/excited state (4 computations).
 
 Even if we use minimal settings, the workflow takes a few minutes to run on one core.

abipy/scripts/abistruct.py

@@ -60,8 +60,8 @@ def get_epilog() -> str:
   abistruct.py abisanitize FILE            => Read structure from FILE, call abisanitize, compare structures
                                               and save "abisanitized" structure to file.
   abistruct.py conventional FILE           => Read structure from FILE, generate conventional structure
-                                              following doi:10.1016/j.commatsci.2010.05.010
-  abistruct.py proto FILE                  => Read structure from FILE, find possible crystallographic prototypes
+                                              following Setyawan, W., & Curtarolo, S. (2010) doi:10.1016/j.commatsci.2010.05.010 
+  abistruct.py proto FILE                  => Read structure from FILE, find possible crystallographic prototypes:
                                               in the AFLOW library of crystallographic prototypes.
                                               See http://doi.org/10.1016/j.commatsci.2017.01.017
 
@@ -290,7 +290,7 @@ def add_format_arg(parser, default, option=True, formats=None):
     # Subparser for conventional.
     p_conventional = subparsers.add_parser('conventional', parents=[copts_parser, path_selector, spgopt_parser, savefile_parser],
         help="Gives a structure with a conventional cell according to certain standards. "
-             "The standards are defined in doi:10.1016/j.commatsci.2010.05.010")
+             "The standards are defined in Setyawan, W., & Curtarolo, S. (2010) doi:10.1016/j.commatsci.2010.05.010")
 
     # Subparser for proto.
     p_proto = subparsers.add_parser('proto', parents=[copts_parser, path_selector],