Remove openbabel dependency in qchem

[soranjh]

Context:
This PR removes the qchem dependency to openbabel which was used for converting different molecular geometry formats to the xyz format. We can safely expect the users to perform such conversions. The PR also collects the general-purpose functions of qml.qchem in a new structure module. All the functions in the new structure module will be still accessible with qml.qchem.function_name.

Description of the Change:
The function read_structure is modified to remove its dependency to openbabel . The functions read_structure, active_space, excitations, hf_state and excitations_to_wires are moved inside structure.

Benefits:
Removing qchem dependencies.

Possible Drawbacks:

Related GitHub Issues:

[github-actions]

Hello. You may have forgotten to update the changelog!
Please edit doc/releases/changelog-dev.md with:

• A one-to-two sentence description of the change. You may include a small working example for new features.
• A link back to this PR.
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[codecov]

Codecov Report

Merging #2415 (79553ff) into master (bce2411) will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #2415      +/-   ##
==========================================
+ Coverage   99.43%   99.45%   +0.02%     
==========================================
  Files         243      244       +1     
  Lines       18987    18971      -16     
==========================================
- Hits        18879    18867      -12     
+ Misses        108      104       -4     

Impacted Files	Coverage Δ
qchem/pennylane_qchem/qchem/__init__.py	100.00% <ø> (ø)
qchem/pennylane_qchem/qchem/openfermion_obs.py	100.00% <100.00%> (+1.50%)	⬆️
qchem/pennylane_qchem/qchem/structure.py	100.00% <100.00%> (ø)

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[obliviateandsurrender]

Looks good to go.

[josh146]

@soranjh do you also need to remove openbabel from the various actions and docs? E.g.,

• .github\workflows\tests.yml
• doc\development\guide\installation.rst
• doc\introduction\chemistry.rst
• docker\qchem.dockerfile
• qchem\install-dependencies.sh
• qchem\README.rst

[soranjh]

@soranjh do you also need to remove openbabel from the various actions and docs? E.g.,

Thanks @josh146. Removed openbabel everywhere.

[josh146]

@soranjh sorry I missed this one! But openbabel was only one of the packages being installed, do we still need make and git? If so, we will need to revert the line to

    && apt-get -y install --no-install-recommends make git \

[soranjh]

Hey Josh. I am actually making my final PR to bring qchem inside pennylane and remove the need for installation. I can create a small PR just to retrieve this line during the few days transition period until that PR gets merged.