Fix/requirements into setuppy

Description

• Removes the requirements.txt file
• Move requirements into setup.py
• Reformat setup.py
• Update README to reflect no longer using requirements.txt
• Update CI to use new setup
  • Generates venv for tests each time to ensure runner local env is not used
  • Added --ignore=tests/legacy flag to pytest to ignore legacy test dir
  • Added --cov=cal_tools and --cov=xfel_calibrate to get coverage output for both modules
  • Added ssh key variable to CI, added .setup-ssh-euxfel-gitlab template to CI
• Change internal dependencies to use SSH instead of files (this is now possible as xsoft has a keypair on gitlab)

These changes make the installation of the package a bit more standard, removes the step of having to run two install commands (one for requirements.txt, and one for .), and let us use extras to define additional optional dependencies (e.g. test, dev, etc...).

How Has This Been Tested?

Tested locally by running pip install without extras, with test, with dev, and with test,dev, then ran the pytests to check that everything was still working correctly.

Also updated the CI definition to use the new setup style, so the tests also executed with the pipeline.

Relevant Documents (optional)

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.

Reviewers

@danilevc @ahmedk @hammerd

Notes:

For our local dependencies the name of the package doesn't match the name of the repository, so I have to explicitly write out the name, and then use the git ssh url as a target, e.g. iCalibrationDB @ git+ssh://git@git.xfel.eu:10022/detectors/cal_db_interactive.git@2.0.1. @kluyvert does this look correct?

README.rst

@@ -223,8 +223,8 @@ Finally run the script:
 
 .. code::
 
-    python3 calibrate.py --input /gpfs/exfel/exp/SPB/201701/p002012/raw/r0100 \
-      --output ../../test_out --mem-cells 30 --detector AGIPD --sequences 0,1
+  python3 calibrate.py --input /gpfs/exfel/exp/SPB/201701/p002012/raw/r0100 \
+    --output ../../test_out --mem-cells 30 --detector AGIPD --sequences 0,1
 
 Here `--input` should point to a directory of `RAW` files for the detector you
 are calibrating. They will be output into the folder specified by `--output`,
@@ -262,37 +262,37 @@ This account is intended to be used as a read only account which can be given
 access to certain repos to make it easier to clone them when using our
 functional accounts on Maxwell.
 
-The xcaltst account has an ed25519 keypair under `~/.ssh/gitlab/`, the public
+The xcaltst account has an ed25519 keypair under ``~/.ssh/gitlab/``, the public
 key has been added to the xcalgitlab's approved SSH keys.
 
-Additionally this block has been added to `~/.ssh/config`:
+Additionally this block has been added to ``~/.ssh/config``:
 
-```
-# Special flags for gitlab over SSH
-Host git.xfel.eu
-    User git
-    Port 10022
-    ForwardX11 no
-    IdentityFile ~/.ssh/gitlab/id_ed25519
-```
+.. code::
+
+  # Special flags for gitlab over SSH
+  Host git.xfel.eu
+      User git
+      Port 10022
+      ForwardX11 no
+      IdentityFile ~/.ssh/gitlab/id_ed25519
 
-Now any repository that `xcalgitlab` has read access to, e.g. if it is added as
+Now any repository that ``xcalgitlab`` has read access to, e.g. if it is added as
 a reporter, can be cloned on Maxwell without having to enter a password.
 
-For example, xcalgitlab is a reporter on the pycalibration
+For example, ``xcalgitlab`` is a reporter on the pycalibration
 https://git.xfel.eu/gitlab/detectors/pycalibration repository, so now
-`xcalgitlab` can do passwordless clones with SSH:
-
-```
-[xcaltst@max-exfl017 tmp]$ git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
-Cloning into 'pycalibration'...
-remote: Enumerating objects: 9414, done.
-remote: Counting objects: 100% (9414/9414), done.
-remote: Compressing objects: 100% (2858/2858), done.
-remote: Total 9414 (delta 6510), reused 9408 (delta 6504)
-Receiving objects: 100% (9414/9414), 611.81 MiB | 54.87 MiB/s, done.
-Resolving deltas: 100% (6510/6510), done.
-```
+``xcalgitlab`` can do passwordless clones with SSH:
+
+.. code::
+
+  [xcaltst@max-exfl017 tmp]$ git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
+  Cloning into 'pycalibration'...
+  remote: Enumerating objects: 9414, done.
+  remote: Counting objects: 100% (9414/9414), done.
+  remote: Compressing objects: 100% (2858/2858), done.
+  remote: Total 9414 (delta 6510), reused 9408 (delta 6504)
+  Receiving objects: 100% (9414/9414), 611.81 MiB | 54.87 MiB/s, done.
+  Resolving deltas: 100% (6510/6510), done.
 
 References: