Merge pull request #435 from haddocking/beta_readme

Update README file for Beta version

README.md

@@ -1,27 +1,42 @@
-# WARNING: The `main` branch is not production-ready
+Welcome to the HADDOCK3-Beta version
 
-The `main` branch is a prototype of newly refined architecture and it
-does not yet contain the functionalities we have reported previously.
-For a running version of HADDOCK3 please refer to the `alpha1` or the
-release page. However, we won't develop `alpha1` further. Stay tuned for
-new updates on the `main` branch as we are actively working on it.
-Cheers!
+The `main` branch represents the latest state of HADDOCK v3. Currently,
+stable beta version.
 
 * * *
 
 # HADDOCK3
 
 ## 1. Installation
 
-To install HADDOCK3 follow the instructions in the [INSTALL](docs/INSTALL.md) file.
+To install HADDOCK3 follow the instructions in the [INSTALL](docs/INSTALL.md)
+file.
+
+## 2. Documentation
+
+HADDOCK3-beta documentation is not yet hosted online. You need to generate it
+locally. First, install HADDOCK3 and activate the `haddock3` python environment
+as explained in the [installation instructions](docs/INSTALL.md). Then, in your
+terminal window, run:
+
+```bash
+tox -e docs
+```
+
+*Ignore any warning messages.* After, use your favorite browser to open the file
+`haddock3-docs/index.html`. This will open a local webpage with the complete
+HADDOCK3 documentation. Navigate around, enjoy, and contribute.
 
 ## 2. Examples
 
 ### 2.1. Basic scoring of an ensemble of 5 structures:
 
+In the `examples/` folder you find several examples for you to test and
+learn HADDOCK3. Additional information is in the documentation pages.
+
 ```bash
-cd examples/recipes/scoring/
-haddock3 scoring.toml
+cd examples/scoring/
+haddock3 emscoring-test.cfg
 ```
 
 ## 3. Contribute
@@ -31,6 +46,12 @@ If you want to contribute to HADDOCK3's development, read the
 
 ## 4. Keep in contact and support us
 
-HADDOCK3 is an academic project supported by various grants, including the EU BioExcel Center of Excellence for Computational Biomolecular Research. HADDOCK3 is fully open-source and free to download. If you clone this repository and use HADDOCK3 for your research, please support us by signing [this Goole form][googleform] if you have not yet done so. This will allow us contact you when needed for HADDOCK3-related issues, and also provide us a mean to demonstrate impact when reporting for grants.
+HADDOCK3 is an academic project supported by various grants, including the EU
+BioExcel Center of Excellence for Computational Biomolecular Research. HADDOCK3
+is fully open-source and free to download. If you clone this repository and use
+HADDOCK3 for your research, please support us by signing [this Google
+form][googleform] if you have not yet done so. This will allow us contact you
+when needed for HADDOCK3-related issues, and also provide us a mean to
+demonstrate impact when reporting for grants.
 
 [googleform]: https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform

tox.ini

@@ -103,8 +103,8 @@ usedevelop = true
 deps =
     -r{toxinidir}/devtools/docs-requirements.txt
 commands =
-    sphinx-build {posargs:-E} -b html docs dist/docs
-    #sphinx-build -b linkcheck docs dist/docs
+    sphinx-build {posargs:-E} -b html docs haddock3-docs
+    #sphinx-build -b linkcheck docs haddock3-docs
 
 # code quality assessment. This is not a check in the CI, serves just
 # as info for the developer