merge readme.md update and do.py from development

README.md

@@ -609,8 +609,8 @@ year = 2021
 }
 ```
 
-Links and Documentation <a name="Links"></a>
------------------------
+Links About the Workshops and Data <a name="Links"></a>
+----------------------------------
 * The [_BBOB workshop series_](http://numbbo.github.io/workshops), which uses the
   NumBBO/Coco framework extensively, can be tracked
   [here](http://numbbo.github.io/workshops "BBOB Workshops")
@@ -623,23 +623,6 @@ Links and Documentation <a name="Links"></a>
   found at https://numbbo.github.io/ppdata-archive
 * Stay informed about the BBOB workshop series and releases of the NumBBO/Coco software 
   by registering via [this form](https://docs.google.com/forms/d/1GS48SXGjapUu6WY6Zt-Ma5HCl2izq4ydT7sMa5ujUDI)
-* Read about the basic principles behind the Coco platform in [COCO: A Platform for Comparing Continuous Optimizers in a Black-Box Setting (pdf)](https://www.tandfonline.com/eprint/DQPF7YXFJVMTQBH8NKR8/pdf?target=10.1080/10556788.2020.1808977) or at [arXiv](https://arxiv.org/abs/1603.08785).
-* For details on the experimental set-up to carry out the benchmarking
-  please refer to http://numbbo.github.io/coco-doc/experimental-setup/.
-* More detailed documentation of the existing benchmark suites can be found here:
-  - for the **`bbob`** problem suite at https://numbbo.github.io/gforge/downloads/download16.00/bbobdocfunctions.pdf 
-    with the experimental setup at http://coco.lri.fr/downloads/download15.03/bbobdocexperiment.pdf
-  - for the **`bbob-biobj`** and **`bbob-biobj-ext`** problem suites
-    at http://numbbo.github.io/coco-doc/bbob-biobj/functions
-  - for the **`bbob-largescale`** problem suite
-    at https://arxiv.org/pdf/1903.06396.pdf
-  - for the **`bbob-mixint`** and **`bbob-biobj-mixint`** problem suites, we refer to 
-    https://hal.inria.fr/hal-02067932/document and to
-    https://numbbo.github.io/gforge/preliminary-bbob-mixint-documentation/bbob-mixint-doc.pdf
-* Online documentation of the NumBBO/Coco API (i.e. for the ANSI C code) is available at 
-  http://numbbo.github.io/coco-doc/C
-* More detailed documentation on how the performance assessement is done can 
-  be found at http://numbbo.github.io/coco-doc/perf-assessment/.
 * Downloading this repository 
   - via the above green "Clone or Download" button or 
   - by typing `git clone https://github.com/numbbo/coco.git` or 
@@ -650,27 +633,27 @@ Comprehensive List of Documentations <a name="Documentations"></a>
 * General introduction: [COCO: A Platform for Comparing Continuous Optimizers in a Black-Box Setting (pdf)](https://www.tandfonline.com/eprint/DQPF7YXFJVMTQBH8NKR8/pdf?target=10.1080/10556788.2020.1808977) or at [arXiv](https://arxiv.org/abs/1603.08785)
 * Experimental setup: http://numbbo.github.io/coco-doc/experimental-setup/
 * Testbeds
-  - bbob: https://numbbo.github.io/gforge/downloads/download16.00/bbobdocfunctions.pdf
-  - bbob-biobj: http://numbbo.github.io/coco-doc/bbob-biobj/functions/
-  - bbob-biobj-ext: http://numbbo.github.io/coco-doc/bbob-biobj/functions/
-  - bbob-noisy (only in old code basis): http://coco.lri.fr/downloads/download15.03/bbobdocnoisyfunctions.pdf
-  - bbob-largescale: https://arxiv.org/pdf/1903.06396.pdf
-  - bbob-mixint and bbob-biobj-mixint: https://hal.inria.fr/hal-02067932/document and
-    https://numbbo.github.io/gforge/preliminary-bbob-mixint-documentation/bbob-mixint-doc.pdf
-  - bbob-constrained (in progress): http://numbbo.github.io/coco-doc/bbob-constrained/functions/
+  - `bbob`: https://numbbo.github.io/gforge/downloads/download16.00/bbobdocfunctions.pdf
+  - `bbob-biobj`: http://numbbo.github.io/coco-doc/bbob-biobj/functions/
+  - `bbob-biobj-ext`: http://numbbo.github.io/coco-doc/bbob-biobj/functions/
+  - `bbob-noisy` (only in old code basis): http://coco.lri.fr/downloads/download15.03/bbobdocnoisyfunctions.pdf
+  - `bbob-largescale`: https://arxiv.org/pdf/1903.06396.pdf
+  - `bbob-mixint`: https://hal.inria.fr/hal-02067932/document
+  - `bbob-biobj-mixint`: https://numbbo.github.io/gforge/preliminary-bbob-mixint-documentation/bbob-mixint-doc.pdf
+  - `bbob-constrained` (in progress): http://numbbo.github.io/coco-doc/bbob-constrained
   
-
 * Performance assessment: http://numbbo.github.io/coco-doc/perf-assessment/
 * Performance assessment for biobjective testbeds: http://numbbo.github.io/coco-doc/bbob-biobj/perf-assessment/
 
 * APIs
   - ``C`` experiments code: http://numbbo.github.io/coco-doc/C
-  - Python experiments code (module `cocoex`): https://numbbo.github.io/gforge/apidocs-cocoex/cocoex.html
-  - Python short [beginners example experiment](code-experiments/build/python/example_experiment_for_beginners.py)
-  - Python `example_experiment2.py`: https://numbbo.github.io/gforge/apidocs-example_experiment/example_experiment2.html
-  - Postprocessing code (module `cocopp`): https://numbbo.github.io/gforge/apidocs-cocopp/cocopp.html
+  - Python experiments code (module `cocoex`): https://numbbo.github.io/coco-doc/apidocs/cocoex
+  - Python [short experiment code example for beginners](code-experiments/build/python/example_experiment_for_beginners.py)
+  - Python [`example_experiment2.py`](https://github.com/numbbo/coco/blob/master/code-experiments/build/python/example_experiment2.py): https://numbbo.github.io/coco-doc/apidocs/example
+  - Postprocessing code (module `cocopp`): https://numbbo.github.io/coco-doc/apidocs/cocopp
 
 * Somewhat outdated documents:
+  - Former home page: https://web.archive.org/web/20210504150230/https://coco.gforge.inria.fr/
   - Full description of the platform: http://coco.lri.fr/COCOdoc/
   - Experimental setup before 2016: http://coco.lri.fr/downloads/download15.03/bbobdocexperiment.pdf
   - Old framework software documentation: http://coco.lri.fr/downloads/download15.03/bbobdocsoftware.pdf

do.py

@@ -51,8 +51,8 @@
 
 ################################################################################
 ## C
-def build_c():
-    """ Builds the C source code """
+def amalgamate_c():
+    """Only amalgamate the C files"""
     global RELEASE
     amalgamate(CORE_FILES + ['code-experiments/src/coco_runtime_c.c'],
                'code-experiments/build/c/coco.c', RELEASE,
@@ -62,17 +62,16 @@ def build_c():
                 {"COCO_VERSION": git_version(pep440=True)})
     copy_file('code-experiments/build/c/coco.c',
               'code-experiments/examples/bbob2009-c-cmaes/coco.c')
-    expand_file('code-experiments/build/c/coco.h',
-                'code-experiments/examples/bbob2009-c-cmaes/coco.h',
-                {'COCO_VERSION': git_version(pep440=True)})
+    copy_file('code-experiments/build/c/coco.h',
+              'code-experiments/examples/bbob2009-c-cmaes/coco.h')
     write_file(git_revision(), "code-experiments/build/c/REVISION")
     write_file(git_version(), "code-experiments/build/c/VERSION")
-    if 11 < 3:
-        python('code-experiments/build/c', ['make.py', 'clean'], verbose=_build_verbosity)
-        python('code-experiments/build/c', ['make.py', 'all'], verbose=_build_verbosity)
-    else:
-        make("code-experiments/build/c", "clean", verbose=_build_verbosity)
-        make("code-experiments/build/c", "all", verbose=_build_verbosity)
+
+def build_c():
+    """ Builds the C source code """
+    amalgamate_c()
+    make("code-experiments/build/c", "clean", verbose=_build_verbosity)
+    make("code-experiments/build/c", "all", verbose=_build_verbosity)
 
 
 def run_c():
@@ -909,6 +908,7 @@ def help():
 
 Available commands for users:
 
+  amalgamate-c            - Amalgamate C module
   build-c                 - Build C module
   build-java              - Build Java module
   build-matlab            - Build Matlab module
@@ -992,6 +992,7 @@ def main(args):
     if cmd == 'build': build(package_install_option = package_install_option)
     elif cmd == 'run': run_all(package_install_option = package_install_option)
     elif cmd == 'test': test(package_install_option = package_install_option)
+    elif cmd == 'amalgamate-c': amalgamate_c()
     elif cmd == 'build-c': build_c()
     elif cmd == 'build-java': build_java()
     elif cmd == 'build-matlab': build_matlab()