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changing the place where the amber environments are called. (#81)

* changing the place where the amber environments are called.

* fix format using black
* new_release

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new_release New_add_doc (#71)

* Avoid simple pass in Exceptions

* Restrict coverage folders in GH action

* Removed ipython from poetry

* Refactored copy_log in cli.py

* How to setup for dev

* Improved exception handling

* Added a janitor fixture for pytest

* Fixed ver_today with pcregrep (linux/macos)

* Remove ipython dev dependency

* Test verboless

* Fixed bug for sorted atomPairs

* Test ILDN with -z exception

* Test ILDN with -z exception improved

* Corrected logger().exception use

* Install poetry via curl

* Pytest in random order

* Test for corrupt glycam

* Added sphinx and docs

* Adding docs, just starting

* Fixed some badges

* Added info about documenting

* Improved doc example

* Trying to refine actions

* Use dynamic year for copyright

* Tests for mol and mdl formats

* Test sqm fails due to wrong charge input

* Typings and docs

* Test for ekFlag

* Try/exception around setResNameCheckCoords()

* Remove try/exception around os.chdir(mol.rootDir)

* Tests about resname

* tests for empty amber files

* Test mol geometry

* Check resname

* convertSmilesToMol2: redundant obabel check

* Increasing coverage about charges

* Fixed regex in ver_today.sh

* Poetry added pyupgrade, pre-commit and sphinx

* Make check_acpype.py to work, still need more

* Pyupgraded

* Added printErrorQuoted

* pre-commit end-of-file-fixer

* pid and docstrings errors cleared

New Logger new_release (#64)

* add loggin

* create log file in tmp path

* add logger file

* remove file and line description in log file

* fix stdout output to pass pytests

* added print function along with logging function; added the logging.exception function to catch the raise exception.

* logger fix to remove redundant prints

* fix handlers

* Refactored logger and cli

* Test -w x -d args

* Decoupled stdout from file log

* Use tempfile for log

* Fixed logic for delOutputFiles()

Co-authored-by: lkagami <lucianopkagami@hotmail.com>

new_release Gaff2 and disambiguate default now

new_release remove leading zeros in version

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