Update installation instructions

README.md

@@ -26,7 +26,34 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**
 
 ## Installation
 
-Please check the [INSTALL](docs/INSTALL.md) file for instructions.
+Clone the repository and run `pip install .`;
+
+```bash
+git clone https://github.com/haddocking/haddock3
+cd haddock3
+pip install .
+```
+
+Execute:
+
+```bash
+$ haddock3 -h
+usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe
+
+positional arguments:
+  recipe                The input recipe file path
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --restart RESTART     Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
+  --extend-run EXTEND_RUN
+                        Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
+  --setup               Only setup the run, do not execute
+  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+  -v, --version         show version
+```
+
+For the installation of third-party additional software, please check the [INSTALL](docs/INSTALL.md).
 
 You might also want to check the following utilities:
 

docs/INSTALL.md

@@ -1,130 +1,31 @@
 # Installation
 
-Open a `terminal` window and navigate to the folder where you want to
-install HADDOCK3; for example: `software`. The current installation
-instructions are local and will affect only your user.
-
-Before starting with the installation of HADDOCK3, make sure to properly [install CNS](CNS.md).
-If you have installed a previous version of HADDOCK, you may already have a suitable version of CNS.
-Please do [check your CNS installation](CNS.md#5-Check-installation) before proceeding.
-
-
-## 1. Clone this repository:
-
-Mind the `--recursive` flag when cloning!
-
-```bash
-git clone --recursive https://github.com/haddocking/haddock3.git
-```
-
-Go to the **haddock3** directory
-
-```bash
-cd haddock3
-```
-
-and type the following commands to first install the [FCC](https://github.com/haddocking/fcc) source code provided
-
-```bash
-cd src/fcc/src
-chmod u+x Makefile
-make
-cd -
-```
-
-Then, follow the same logic to install the [fast-rmsdmatrix](https://github.com/mgiulini/fast-rmsdmatrix) source code
-
-```bash
-cd src/fast-rmsdmatrix/src
-chmod u+x Makefile
-make fast-rmsdmatrix
-cd -
-```
-
-By the end of the above commands, you should be back to the **haddock3**
-main folder.
-
-## 2 Create a virtual environment with Python 3.9+ and install dependencies:
+Create a virtual environment with Python 3.9:
 
 You can use Python's `venv` or `conda` depending on your choice.
 Commands are provided below:
 
 ### with `venv`
 
 ```bash
-virtualenv venv --python=3.9
-source venv/bin/activate
-pip install -r requirements.txt
+python -m venv .venv
+source .venv/bin/activate
 ```
 
 ### with `conda`
 
 ```bash
 conda create -n haddock3 python=3.9
 conda activate haddock3
-pip install -r requirements.txt
-```
-
-## 3. Install the HADDOCK3 package and command line clients
-
-```bash
-python setup.py develop --no-deps
-```
-
-Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS.
-
-## 4. Make a CNS binary shortcut to the expected path:
-
-```bash
-mkdir -p bin/
-
-# on mac
-ln -s /PATH/TO/cns_solve_1.3/mac-intel-darwin/source/cns_solve-2206031450.exe bin/cns
-
-# on linux
-ln -s /PATH/TO/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns
-```
-
-As long as you have the `(haddock3)` python environment activated, you can
-navigate away from the **haddock3** installation folder. You can run
-HADDOCK3 from anywhere. To run HADDOCK3, follow the [usage
-guidelines](USAGE.md).
-
-
-## 5. Keep your installation up to date
-
-Navigate to the **haddock3** installation folder (the one you cloned from
-GitHub). Ensure you have the `(haddock3)` python environment activated.
-Please keep in mind that HADDOCK3, as well as its
-dependencies, are under active development.
-If the updating processing fails, it is safest to reinstall
-from scratch. Always refer to the latest installation guidelines.
-
-```bash
-# if you used `venv`
-source venv/bin/activate
-
-# if you used `conda`
-conda activate haddock3
 ```
 
-Afterwards:
-
 ```bash
-# pull the latest source code from our repository to your computer
-git pull
-
-# update the dependencies by running:
-pip install -r requirements.txt  --upgrade
-
-# ensure all command-lines clients are installed
-python setup.py develop --no-deps
+git clone https://github.com/haddocking/haddock3.git
+cd haddock3
+pip install .
 ```
 
-Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS.
-
-
-## 6. (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI
+## (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI
 
 To use the mpi implementation of haddock3 you must have mpi4py installed in the `(haddock3)` python environment, and OpenMPI in the host system.
 
@@ -136,7 +37,7 @@ $ conda install -c conda-forge mpi4py
 
 Later, you can find [here](https://www.bonvinlab.org/haddock3/tutorials/mpi.html) instructions on how to run HADDOCK3 with MPI.
 
-## 7. (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service
+## (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service
 
 To run the restraints web service you must have the following dependencies installed in the `(haddock3)` python environment:
 
@@ -146,21 +47,21 @@ pip install uvicorn fastapi
 
 Information on the restraints web service can be found [here](https://github.com/haddocking/haddock3/blob/main/src/haddock/clis/restraints/webservice.py).
 
-# Installing third-party packages
+## Installing third-party packages
 
 HADDOCK3 can integrate third-party software in its workflows.
 We are not responsible for the proper installation of such packages, but
 we help you install them. Below, you will find a list of all third-party
 packages HADDOCK3 can use and guidelines for their proper installation.
 
-## `lightdock`
+### `lightdock` (outdated)
 
 To install [lightdock](https://github.com/lightdock/lightdock) follow
 the instructions on the project's website. Remember to install it under
 the same Python environment you created for HADDOCK3. If you have any
 doubts, please let us know.
 
-## `gdock`
+### `gdock` (outdated)
 
 1. Clone the latest version:
 
@@ -170,11 +71,13 @@ git clone https://github.com/rvhonorato/gdock.git
 ```
 
 2. Install Python3+ dependencies
+
 ```
 pip install deap scipy mgzip biopython
 ```
 
 3. Set `GDOCK_PATH`
+
 ```
 export GDOCK_PATH=some-folder
 ```

src/haddock/clis/cli.py

@@ -36,10 +36,13 @@
 ap = argparse.ArgumentParser()
 
 ap.add_argument(
-    "recipe",
+    "workflow",
     type=arg_file_exist,
-    help="The input recipe file path",
-)
+    help=(
+        "The input configuration file path describing "
+        "the workflow to be performed"
+        ),
+    )
 
 add_restart_arg(ap)
 add_extend_run(ap)
@@ -76,7 +79,7 @@ def maincli() -> None:
 
 
 def main(
-    recipe: FilePath,
+    workflow: FilePath,
     restart: Optional[int] = None,
     extend_run: Optional[FilePath] = EXTEND_RUN_DEFAULT,
     setup_only: bool = False,
@@ -87,8 +90,8 @@ def main(
 
     Parameters
     ----------
-    recipe : str or pathlib.Path
-        The path to the recipe (config file).
+    workflow : str or pathlib.Path
+        The path to the workflow (config file).
 
     restart : int
         The step to restart the run from (inclusive).
@@ -145,7 +148,7 @@ def main(
 
     with log_error_and_exit():
         params, other_params = setup_run(
-            recipe,
+            workflow,
             restart_from=restart,
             extend_run=extend_run,
         )

tests/test_cli.py

@@ -8,7 +8,9 @@
 from . import configs_data
 
 
-recipe = Path(configs_data, 'recipe.cfg')
+@pytest.fixture(name="workflow")
+def fixture_workflow():
+    yield Path(configs_data, "recipe.cfg")
 
 
 def test_cli_has_maincli():
@@ -21,29 +23,29 @@ def test_cli_has_maincli():
 
 
 def test_ap_recipe_does_not_exist():
-    """Test raise error if recipe does not exist."""
+    """Test raise error if workflow does not exist."""
     with pytest.raises(SystemExit) as exit:
         cli.ap.parse_args('does_not_exit.cfg'.split())
     assert exit.type == SystemExit
     assert exit.value.code == 2
 
 
-def test_ap_recipe_exists():
-    """Test reading recipes."""
-    cmd = cli.ap.parse_args(str(recipe).split())
-    with open(cmd.recipe) as fin:
+def test_ap_workflow_exists(workflow):
+    """Test reading workflows."""
+    cmd = cli.ap.parse_args(str(workflow).split())
+    with open(cmd.workflow) as fin:
         fin.readlines()
 
 
-def test_ap_setup_true():
+def test_ap_setup_true(workflow):
     """Test --setup flag."""
-    cmd = cli.ap.parse_args(f'{recipe} --setup'.split())
+    cmd = cli.ap.parse_args(f'{workflow} --setup'.split())
     assert cmd.setup_only is True
 
 
-def test_ap_setup_false():
+def test_ap_setup_false(workflow):
     """Test setup only default."""
-    cmd = cli.ap.parse_args(str(recipe).split())
+    cmd = cli.ap.parse_args(str(workflow).split())
     assert cmd.setup_only is False
 
 
@@ -59,15 +61,15 @@ def test_ap_version():
     'level',
     ("DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"),
     )
-def test_ap_log_level(level):
+def test_ap_log_level(workflow, level):
     """Test --log-level correct."""
-    cmd = cli.ap.parse_args(f'{recipe} --log-level {level}'.split())
+    cmd = cli.ap.parse_args(f'{workflow} --log-level {level}'.split())
     assert cmd.log_level == level
 
 
-def test_ap_log_level_error():
+def test_ap_log_level_error(workflow):
     """Test --log-level error with bad input."""
     with pytest.raises(SystemExit) as exit:
-        cli.ap.parse_args(f'{recipe} --log-level BAD'.split())
+        cli.ap.parse_args(f'{workflow} --log-level BAD'.split())
     assert exit.type == SystemExit
     assert exit.value.code == 2