rinikerlab / PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.
https://rinikerlab.github.io/PyGromosTools/
MIT License
16 stars 14 forks source link

pleasing pep8 #237

Closed RiesBen closed 2 years ago

RiesBen commented 2 years ago

Description

fixing Wrappers and making sure the tutorial jnb and hvap jnb work

codecov[bot] commented 2 years ago

Codecov Report

Merging #237 (e227fb5) into release3 (1990f5d) will decrease coverage by 0.03%. The diff coverage is 61.55%.

@@             Coverage Diff              @@
##           release3     #237      +/-   ##
============================================
- Coverage     54.63%   54.60%   -0.04%     
============================================
  Files            92       92              
  Lines         13884    14034     +150     
============================================
+ Hits           7586     7663      +77     
- Misses         6298     6371      +73     
Flag Coverage Δ
unittests 54.60% <61.55%> (-0.04%) :arrow_down:

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

Impacted Files Coverage Δ
pygromos/files/coord/cnf.py 44.33% <ø> (-0.76%) :arrow_down:
...ns/approaches/hvap_calculation/hvap_calculation.py 0.00% <0.00%> (ø)
...ng/workers/analysis_workers/simulation_analysis.py 12.12% <ø> (-0.38%) :arrow_down:
...imulations/hpc_queuing/submission_systems/dummy.py 81.25% <ø> (ø)
...s/simulations/modules/preset_simulation_modules.py 58.82% <ø> (ø)
pygromos/utils/bash.py 27.71% <0.00%> (-0.08%) :arrow_down:
...orkers/simulation_workers/simulation_run_worker.py 12.50% <6.25%> (-0.71%) :arrow_down:
pygromos/files/trajectory/tre.py 47.44% <33.33%> (+0.38%) :arrow_up:
pygromos/gromos/_gromosClass.py 46.15% <36.36%> (-34.50%) :arrow_down:
.../job_scheduling/schedulers/simulation_scheduler.py 64.58% <44.44%> (+0.37%) :arrow_up:
... and 18 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 1990f5d...e227fb5. Read the comment docs.

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 2 when merging ec0e780f9e42a9a6fa5ce67ef24afa3e2645e484 into 1990f5d73978bf605bbea0f0c31b6352c883982f - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 2 when merging febf56b60fbc0652e4ebbc98aae44a64c0db7da5 into 1990f5d73978bf605bbea0f0c31b6352c883982f - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 2 when merging bd6b0887af59e2d64d182227666ace500edd8b5f into f2239257523fd327980084ed87f6cf9ae40b60ca - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 2 when merging 6138f68e027c0fdb010418ffeb6be015a8611d62 into 80ba1eddaeabc1ea7b4b7d3193fc35d916ca2736 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 2 when merging 3986af29ec35d2bee38fb50f521b057018aaab77 into 80ba1eddaeabc1ea7b4b7d3193fc35d916ca2736 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 2 alerts and fixes 2 when merging fc1aa999d14787d9faf4a66a87c433109c2af9e0 into 80ba1eddaeabc1ea7b4b7d3193fc35d916ca2736 - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 7b8ff8a73bfb1a382acead1e9784c9534d803fc9 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 3 when merging de94ab802f3e7fe653733ad551b5f8b52f67adff into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 1 alert and fixes 3 when merging c712b739c376a96b92845cd81f530cb7422750e9 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 16 alerts and fixes 3 when merging 2bdd42c6dc21a13488eae1f82b9d28b11eea0c8a into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 17 alerts and fixes 3 when merging 98129bec9802d3c9a37ce9a8b7f6a249b8767b90 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 2 alerts and fixes 3 when merging 98c3673c2404f5e56454e51c5e568a5ad4e9de0a into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 2 alerts and fixes 3 when merging fc83208bbdc03fa57ec0d14f48e7d80b2838561e into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 329751eba84fb6447b4fad4e7f411de194e17857 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 2 alerts and fixes 3 when merging e41af144cffe1737c1b9838a9f8e7849a7c2480c into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 17 when merging 55d56c57deed9d090da1353fda0b4f945747dd71 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 4 alerts and fixes 3 when merging 34aa7f9a00d07cf41d57f8659c87b79db618a60f into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 4 alerts and fixes 3 when merging e66c2bd77ae34214135ebf1a33ed5a6c993d0588 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 4 alerts and fixes 3 when merging c7a553a0e03d7b614a0090881612fc288c854bb2 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 4 alerts and fixes 3 when merging f2bef77405e7a720a3d1c9c77c43256878dc3ae5 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 4 alerts and fixes 3 when merging 56a30011cf1265a30af5f62a1bbf864aebf74dda into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 1d7e2f620b8301a7eeb473f8fb41b95d79c55396 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 310ba076ab724c72ae0c88ceae93a570556d0b69 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging bf1145f11cfa2ebccc05152ef4e756a10a0686ff into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 4015b6f67c5d02eed04a29c6f0af0a05353c6a7a into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 6e11a59db079914ba0b7b80cafd64eeee30383f7 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging c98c65e464fa83915fbec0df4b7b557dae8a2473 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 329be66a4cf381330b19e79f73378251173db776 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging 778c70ccdecedb04c734cd8ba04ec462e56956fe into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging 90ff43b97b627ff7cae8e173a304e7711dd68c1b into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging 0ff15b031422e21473bb3dfc5a24247a6ebdf9a4 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging c1398c1f44892ebffd9047be59a428d80016853c into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging d6e39187308156b98226295fdfc90c520d02a208 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging 3f71342bf5d4617d40cac25640759acdfbb4a96f into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 5 alerts and fixes 3 when merging 94a70362f35ce824d1a72341af316709a622dfef into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging ba8ef2bee7078ade6fa3be2347c4e19abb92f255 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 8e53db736134fb48a434453552bbeb4767dd3745 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging a86511546ba9b7a183f03d399d5c9ed9d2b09cd2 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging ba564a5c74a6e3798158a41630e8eea256bc6538 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 188c4f5904251d2c54bc3bf81918e4fa5304ad1c into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

MTLehner commented 2 years ago

@SchroederB

TODOs:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging af10caec2c9740f39394ad0a2680573d6ba9bd44 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging a2490a539047013eb40c55adabf3a2fcdc56365d into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 6c0cc0080e3621a11fc2d28a7f29326828573595 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 66c63deae10960948432c65cd3818d9849bd623e into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 6fd7fffa2de8845208e7608545247c0ed8a6ac9a into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging acd9aa34783f66f21d4d3b42a0776232ec0d29f9 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging c25e98a556414eebcf30d6408abe2f28eb72f748 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 3 alerts and fixes 3 when merging 77d4a80a49afc69101dde9e0e684dfa12db78a99 into 7e3a9f4a7d8a9520ad784697b45b0d90dcdf6c2e - view on LGTM.com

new alerts:

fixed alerts: