Feature/combine cli

[97gamjak]

Added a combined cli interface

closes #40

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 68.69159% with 67 lines in your changes are missing coverage. Please review.

Project coverage is 80.33%. Comparing base (4913831) to head (d041b18). Report is 1 commits behind head on dev.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #49 +/- ## ========================================== + Coverage 80.23% 80.33% +0.10% ========================================== Files 119 121 +2 Lines 4411 4562 +151 ========================================== + Hits 3539 3665 +126 - Misses 872 897 +25 ``` | [Flag](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | `80.33% <68.69%> (+0.10%)` | :arrow_up: | | [Files](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | Coverage Δ | | |---|---|---| | [PQAnalysis/cli/\_argument\_parser.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2F_argument_parser.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvX2FyZ3VtZW50X3BhcnNlci5weQ==) | `91.83% <100.00%> (-1.79%)` | :arrow_down: | | [PQAnalysis/cli/\_cli\_base.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2F_cli_base.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvX2NsaV9iYXNlLnB5) | `100.00% <100.00%> (ø)` | | | [PQAnalysis/cli/continue\_input.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Fcontinue_input.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvY29udGludWVfaW5wdXQucHk=) | `96.55% <94.44%> (-3.45%)` | :arrow_down: | | [PQAnalysis/cli/rst2xyz.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Frst2xyz.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvcnN0Mnh5ei5weQ==) | `96.66% <94.44%> (-3.34%)` | :arrow_down: | | [PQAnalysis/cli/traj2box.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Ftraj2box.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvdHJhajJib3gucHk=) | `96.55% <94.11%> (-3.45%)` | :arrow_down: | | [PQAnalysis/cli/traj2qmcfc.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Ftraj2qmcfc.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvdHJhajJxbWNmYy5weQ==) | `96.42% <93.75%> (-3.58%)` | :arrow_down: | | [PQAnalysis/cli/rdf.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Frdf.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvcmRmLnB5) | `79.41% <66.66%> (+2.13%)` | :arrow_up: | | [PQAnalysis/cli/gen2xyz.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Fgen2xyz.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvZ2VuMnh5ei5weQ==) | `66.66% <55.55%> (+11.11%)` | :arrow_up: | | [PQAnalysis/cli/xyz2gen.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Fxyz2gen.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkveHl6Mmdlbi5weQ==) | `66.66% <55.55%> (+11.11%)` | :arrow_up: | | [PQAnalysis/cli/main.py](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree&filepath=PQAnalysis%2Fcli%2Fmain.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse#diff-UFFBbmFseXNpcy9jbGkvbWFpbi5weQ==) | `64.28% <64.28%> (ø)` | | | ... and [2 more](https://app.codecov.io/gh/MolarVerse/PQAnalysis/pull/49?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=MolarVerse) | |

[github-actions[bot]]

PYLINT REPORT

Your code has been rated at 9.86/10 (previous run: 9.86/10, +0.00)

Full report

Raw metrics =========== |type |number |% |previous |difference | |----------|-------|------|---------|-----------| |code |6971 |39.06 |6789 |+182.00 | |docstring |8198 |45.93 |7921 |+277.00 | |comment |269 |1.51 |269 |= | |empty |2411 |13.51 |2349 |+62.00 | Duplication =========== | |now |previous |difference | |-------------------------|------|---------|-----------| |nb duplicated lines |0 |0 |0 | |percent duplicated lines |0.000 |0.000 |= | Messages by category ==================== |type |number |previous |difference | |-----------|-------|---------|-----------| |convention |0 |0 |0 | |refactor |43 |43 |43 | |warning |16 |16 |16 | |error |0 |0 |0 | Messages ======== |message id |occurrences | |-----------------------------|------------| |too-many-arguments |18 | |too-many-instance-attributes |10 | |fixme |10 | |duplicate-code |4 | |too-many-locals |3 | |too-complex |3 | |unused-argument |2 | |too-many-branches |2 | |protected-access |2 | |unused-import |1 | |too-many-statements |1 | |too-many-return-statements |1 | |too-many-public-methods |1 | |broad-exception-raised |1 |