Merge pull request #14 from pm-blanco/33-create-folder-paper

Add CI for peptides and clean-up folder structure

.github/workflows/testsuite.yml

@@ -29,6 +29,6 @@ jobs:
         run: |
           module load ESPResSo/4.2.1-foss-2023a
           source pymbe/bin/activate
-          make testsuite
+          make tests
           deactivate
         shell: bash

CONTRIBUTING.md

@@ -10,7 +10,7 @@ To contribute to the pyMBE library, first one needs to be added as a member of t
 If you want to contribute to the development of the pyMBE library, please contact Dr. Pablo M. Blanco (pablb@ntnu.no)
 
 ## Rules to contribute to pyMBE
-Any new version of the code must reproduce all the data stored in `reference_data/`. 
-The scripts provided in `tests/` can be used to quickly set-up  simulations with pyMBE to reproduce such data sets.
+Any new version of the code must reproduce all the data stored in `testsuite/data`. 
+The scripts provided in `testsuite/` and in `samples/Beyer2024` can be used to quickly set-up simulations with pyMBE to reproduce such data sets.
 All new code will be reviewed by at least one member of the pyMBE development team before being merged into the stable version of the library to ensure that a functional version of the code is always available.
 Class methods are sorted in alphabetical order.

Makefile

@@ -2,15 +2,13 @@
 .PHONY: sample
 .PHONY: visual 
 .PHONY: clean
-.PHONY: tests
-.PHONY: testsuite
 .PHONY: docs
 
 docs:
 	pdoc ./pyMBE.py -o ./docs --docformat google 
 
-testsuite:
-	python3 testsuite/LYS_ASP_peptide.py
+tests:
+	python3 testsuite/peptide_tests.py
 
 sample:
 	python3 sample_scripts/peptide_simulation_example.py
@@ -19,15 +17,5 @@ visual:
 	python3 handy_scripts/vmd-traj.py
 	vmd -e visualization.tcl
 
-tests_peptide:
-	python3 tests/LYS_ASP_peptide.py
-	python3 tests/GLU_HIS_peptide.py
-	python3 tests/histatin5_peptide.py
-
-tests_globular_protein:
-	python3 tests/run_test_protein.py --pdb_code 1beb --run_command "python3 sample_scripts/globular_protein.py  --pdb 1beb --path_to_cg reference_parameters/coarse_grained_structures/1beb.vtf"
-	python3 tests/run_test_protein.py --pdb_code 1f6s --run_command "python3 sample_scripts/globular_protein.py  --pdb 1f6s --metal_ion_name Ca --metal_ion_charge 2 --path_to_cg reference_parameters/coarse_grained_structures/1f6s.vtf"
-
-tests:
-	make tests_peptide
-	make tests_globular_protein
+tutorial:
+	jupyter-lab tutorials/pyMBE_tutorial.ipynb

README.md

@@ -20,20 +20,19 @@ A deprecated version of pyMBE compatible with ESPResSo v4.1.4 (under the histori
 
 - `docs/`: folder with the API documentation of pyMBE.
 - `figs/`: folder with various images used in the tutorials of pyMBE.
-- `handy_scripts/`: folder with various handy scripts and libraries.
+- `libs/`: folder with various libraries.
 - `logo/`: folder with the logo of pyMBE.
-- `mantainer/`: folder with various scripts used by the mantainers.
-- `reference_data/`: folder with various reference data set used to validate pyMBE.
-- `reference_parameters/`: folder with various sets of parameters from previous works.
-- `sample_scripts/`: folder with various sample scripts showcasing how to use pyMBE to setup different systems.
-- `tests/`: folder with several test scripts to check that new developments do not break pyMBE.
+- `maintainer/`: folder with various scripts used by the maintainers.
+- `parameters/`: folder with various sets of parameters from previous works.
+- `samples/`: folder with various sample scripts showcasing how to use pyMBE to setup different systems.
 - `testsuite/`: folder with several test scripts and data for continous integration of the library.
 - `tutorials/`: folder with the available tutorials on pyMBE.
 - `visualization/`: folder with helper scripts to aid the visualization of vtf trajectories from constant pH and Grand reaction simulations with [VMD](https://www.ks.uiuc.edu/Research/vmd/).
 - `AUTHORS.md`: list of authors and contributors of pyMBE.
 - `CONTRIBUTING`: rules on how to contribute to pyMBE.
 - `LICENSE.md`: license of pyMBE.
 - `pyMBE.py`: source code of pyMBE
+- `requirements.txt`: list of required libraries to use pyMBE.
 
 ## Usage