Gromos modules

[RiesBen]

Description

This PR will add:

• Hooks to the Gromos repositories (authentification required!)
• a script, that automatically compiles gromos and integrates it into the local repository
• an adapted condaEnv, that allows compiling gromos from the python env.

if you want to try it out, do this: python dev/build_pygromosfully.py

But this might take some time, as compiling Gromos takes >10min

Timings:

conda environment INSTALL: 13min

GromosPP INSTALL (1core):

• Configure: 15s
• Make: 13min

GromosXX INSTALL (1core):

• Configure: 1min
• Make: 9min

known issues:

• [ ] Could not compile GromosPP on euler due to GSL - dependencies problems.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [ ] Test the different compile options.
• [ ] make a compiled binary folder automatically detectable by pyGromosClasses

[lgtm-com[bot]]

This pull request introduces 30 alerts and fixes 104 when merging 5f7e14d9271f93d80308fe4e900fef5ce3ad2881 into 3bb489f7f9c94f3323307c23a435015ad8bd9473 - view on LGTM.com

new alerts:

• 14 for `__eq__` not overridden when adding attributes
• 4 for Unused local variable
• 4 for Modification of parameter with default
• 3 for Variable defined multiple times
• 1 for First parameter of a method is not named 'self'
• 1 for Syntax error
• 1 for Module is imported with 'import' and 'import from'
• 1 for Redundant assignment
• 1 for Wrong number of arguments in a call

fixed alerts:

• 23 for Unused local variable
• 21 for Unused import
• 20 for Testing equality to None
• 18 for Except block handles 'BaseException'
• 9 for 'import *' may pollute namespace
• 4 for Modification of parameter with default
• 2 for `__eq__` not overridden when adding attributes
• 2 for Unreachable code
• 2 for Variable defined multiple times
• 1 for Module is imported more than once
• 1 for Non-callable called
• 1 for Suspicious unused loop iteration variable

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 3 when merging 5f7e14d9271f93d80308fe4e900fef5ce3ad2881 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 1 for First parameter of a method is not named 'self'
• 1 for Syntax error
• 1 for Variable defined multiple times
• 1 for Redundant assignment

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 6 alerts and fixes 3 when merging e19c59af0987d293e9a26a72bd2b7fd1c7eec983 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 2 for Unused import
• 1 for First parameter of a method is not named 'self'
• 1 for Unused local variable
• 1 for Variable defined multiple times
• 1 for Redundant assignment

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 3 when merging d64465c537eb7d7c83a214f02d12f87f7bb47cec into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 1 for First parameter of a method is not named 'self'
• 1 for Variable defined multiple times
• 1 for Redundant assignment
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 3 when merging 09e0516eecaab13cd01cc0f24a5a80a387841c6e into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

• 1 for First parameter of a method is not named 'self'
• 1 for Variable defined multiple times
• 1 for Redundant assignment
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Unnecessary pass
• 1 for Non-callable called
• 1 for Wrong number of arguments in a call

[codecov[bot]]

Codecov Report

Merging #240 (bdc5e97) into release3 (95e5e91) will decrease coverage by 0.39%. The diff coverage is 54.40%.

@@             Coverage Diff              @@
##           release3     #240      +/-   ##
============================================
- Coverage     54.73%   54.34%   -0.40%     
============================================
  Files            91       93       +2     
  Lines         14148    14304     +156     
============================================
+ Hits           7744     7773      +29     
- Misses         6404     6531     +127     

Flag	Coverage Δ
unittests	54.34% <54.40%> (-0.40%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pygromos/analysis/energy_analysis.py	50.00% <ø> (ø)
pygromos/files/forcefield/amber/amberff.py	0.00% <0.00%> (ø)
pygromos/files/forcefield/serenityff/serenityff.py	0.00% <0.00%> (ø)
pygromos/files/otherfiles/new_repdat.py	0.00% <0.00%> (ø)
pygromos/files/otherfiles/noe_output.py	0.00% <ø> (ø)
pygromos/files/trajectory/trg.py	100.00% <ø> (ø)
pygromos/gromos/pyGromosPP/com_top.py	0.00% <0.00%> (ø)
pygromos/gromos/pyGromosPP/ran_box.py	87.50% <ø> (ø)
...ns/approaches/hvap_calculation/hvap_calculation.py	0.00% <0.00%> (ø)
...ons/hpc_queuing/job_scheduling/module_functions.py	0.00% <0.00%> (ø)
... and 61 more

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[RiesBen]

@MTLehner : this change works on my local machine without any problems. On Euler, I managed to compile gromosXX in a standard version. However gromosPP has issues with finding the GSL-library (even though I provided on configure, and there it is found!)