Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark (#4021)

* replace http with https, all committed changes verified

* replace more http with https

* replace expired abinit urls

* replace scipy expired url

* update NIST url and w3.org

* update netCDF4 doc url

* replace some http with https in unit test

* remove debug leftover

* add missing build doc dependency

* rebuild docs

* add invoke to docs dependency

* Revert "rebuild docs" as it makes it impossible to review

This reverts commit 47e4d59.

* revert replace on io.exciting

* revert replacement for structureNL metadata

* fix from pytest import raises or mark

* directly access MonkeyPatch when pytest is already imported

* regenerate documents

Author: DanielYang59

ADMIN.md

@@ -16,7 +16,7 @@ The general procedure for releasing `pymatgen` comprises the following steps:
 
 ## Initial setup
 
-Pymatgen uses [invoke](http://pyinvoke.org) to automate releases.
+Pymatgen uses [invoke](https://pyinvoke.org) to automate releases.
 You will also need `sphinx` and `doc2dash`.
 
 ```sh

CITATION.cff

@@ -5,7 +5,7 @@ message: |
 
   In addition, some of pymatgen's functionality is based on scientific advances
   / principles developed by the computational materials scientists in our team.
-  Please refer to pymatgen's docs at http://pymatgen.org on how to cite them.
+  Please refer to pymatgen's docs at https://pymatgen.org on how to cite them.
 authors:
 - family-names: Ong
   given-names: Shyue Ping

dev_scripts/nist_codata.txt

@@ -2,7 +2,7 @@
              Fundamental Physical Constants --- Complete Listing
 
 
-  From:  http://physics.nist.gov/constants
+  From:  https://physics.nist.gov/cuu/Constants/index.html