Merge pull request plumed#1269 from plumed/readd-installation

Final steps in creation of new manual

Author: gtribello

.ci/requirements.txt

@@ -0,0 +1,7 @@
+Cython
+numpy
+pytest
+six
+pandas
+mdtraj
+MDAnalysis

.github/workflows/linuxWF.yml

@@ -105,7 +105,7 @@ jobs:
         pip install requests
         pip install PlumedToHTML
         pip install networkx
-        pip install mkdocs
+        pip install mkdocs-material
         pip install python-markdown-math
         sudo apt-get install -y graphviz
         sudo apt-get install -y doxygen-latex
@@ -197,6 +197,7 @@ jobs:
         GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
       if: contains( matrix.variant, '-doc-' )
       run: |
+         export PLUMED_MAXBACKUP=0 
          make doc >/dev/null
     - name: Coverage
       env:

CHANGES/v2.0.md

@@ -1,10 +1,9 @@
-@page CHANGES-2-0 Version 2.0
-
 Version 2.0.0 (September 27, 2013)
 ----------------------------
 
 Version 2.0 is a complete rewrite, so there is no way to write a complete set of difference
 with respect to plumed 1.3. Here is a possibly incomplete summary of the difference:
+
 - The input is simpler, more flexible, and more error proof.
   Many checks are now performed and in this way common errors are avoided. 
 - The units are now the same for all MD codes.
@@ -26,6 +25,7 @@ with respect to plumed 1.3. Here is a possibly incomplete summary of the differe
   other.
 
 In addition, it is now much easier to contribute new functionality to the code because: 
+
 - There is a much simpler interface between plumed and the base MD codes.
   This makes it much easier to add plumed to a new MD code. Hopefully, in the future,
   interfaces with MD codes will be maintained by the developers of the MD codes
@@ -38,6 +38,7 @@ In addition, it is now much easier to contribute new functionality to the code b
 - User documentation is provided together inside the implementation files.
 
 Caveats:
+
 - PLUMED 2 input file (plumed.dat) has a syntax which is not
   compatible with PLUMED 1.
   Transition should be easy, but cannot
@@ -46,73 +47,76 @@ Caveats:
 - PLUMED 2 may not include all the features that were available
   in PLUMED 1.
 
-A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see \ref moving).
+A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see [here](https://www.plumed.org/doc-v2.0/user-doc/html/moving.html)).
 
 Version 2.0.1 (Nov 14, 2013)
 ----------------------------
 
-For users:
-- Fixed a bug in \ref HISTOGRAM with REWEIGHT_BIAS. Reweighting was only done when also temperature-reweighting was enabled.
+### For users:
+
+- Fixed a bug in [HISTOGRAM](HISTOGRAM.md) with REWEIGHT_BIAS. Reweighting was only done when also temperature-reweighting was enabled.
 - Fixed a bug that was sometime crashing code with domain decomposition and
   non-dense simulation boxes (e.g. implicit solvent).
-- Performance improvements for \ref GYRATION.
-- Flush all files every 10000 steps by default, without need to use \ref FLUSH
-- Errors when writing input for \ref switchingfunction are now properly
-  recognized.
-- Added message when \ref simplemd is used on a non-existing file.
-- Fixed `plumed mklib` such that it deletes the target shared library in case
-  of compilation error.
+- Performance improvements for [GYRATION](GYRATION.md).
+- Flush all files every 10000 steps by default, without need to use [FLUSH](FLUSH.md)
+- Errors when writing input for switching functions are now properly recognized.
+- Added message when [simplemd](simplemd.md) is used on a non-existing file.
+- Fixed `plumed mklib` such that it deletes the target shared library in case of compilation error.
 - Several small fixes in documentation and log file.
 
-For developers:
+### For developers:
+
 - Added possibility to setup replica exchange from MD codes in Fortran (commands "GREX setMPIFIntercomm" and "GREX setMPIFIntracomm").
 - cmd("setStopFlag") should now be called after PLUMED initialization.
 - Several small fixes in documentation.
 
 Version 2.0.2 (Feb 11, 2014)
 ----------------------------
 
-For users:
-- Fixed bug with \ref METAD with INTERVAL and replica exchange, including bias exchange.
+### For users:
+
+- Fixed bug with [METAD](METAD.md) with INTERVAL and replica exchange, including bias exchange.
   Now the bias is correctly computed outside the boundaries. Notice that this is different
   from what was done in PLUMED 1.3. Also notice that INTERVAL now works
   correctly with grids and splines.
-- Fixed bug with \ref READ and periodic variables.
-- Fixed bug with \ref HISTOGRAM (option USE_ALL_DATA was not working properly).
+- Fixed bug with [READ](READ.md) and periodic variables.
+- Fixed bug with [HISTOGRAM](HISTOGRAM.md) (option `USE_ALL_DATA` was not working properly).
 - Gromacs patch updated to 4.6.5.
-- Gromacs patch for 4.6 has been modified to allow for better load balancing when
-  using GPUs.
+- Gromacs patch for 4.6 has been modified to allow for better load balancing when using GPUs.
 - Added option 'plumed info --long-version' and 'plumed info --git-version'.
 - Added full reference (page/number) to published paper in doc and log.
 - Fixed a bug in file backups (only affecting Windows version - thanks to T. Giorgino).
 - Added possibility to search in the documentation.
 - Several small fixes in documentation and log file.
 
-For developers:
-- Fixed Makefile dependencies in some auxiliary files in src/lib (*cmake and *inc).
-- Changed way modules are linked in src/.
-  E.g. src/colvar/tools/ is not anymore a symlink to src/colvar but a real directory.
+### For developers:
+
+- Fixed Makefile dependencies in some auxiliary files in src/lib (`*cmake` and `*inc`).
+- Changed way modules are linked in `src/`.
+  E.g. `src/colvar/tools/` is not anymore a symlink to `src/colvar` but a real directory.
   (Notice that this introduces a regression: when using plumed as an external library
   some include files could not work - this only applies when plumed is installed;
   also notice that this is fixed in 2.0.3)
 - Patch for gromacs 4.6 now also include original code so as to simplify its modification.
-- Added option 'plumed patch --save-originals'.
-- Fixed regtest regtest/secondarystructure/rt32 to avoid problems with NUMERICAL_DERIVATIVES.
+- Added option `plumed patch --save-originals`.
+- Fixed regtest regtest/secondarystructure/rt32 to avoid problems with `NUMERICAL_DERIVATIVES`.
 - Removed include graphs in the documentation (too large).
 - Several small fixes in documentation.
 
 Version 2.0.3 (June 30, 2014)
 ----------------------------
 
-For users:
+### For users:
+
 - Now compiles on Blue Gene Q with IBM compilers.
-- Fixed bug in \ref CENTER where default WEIGHTS were missing. 
-- Fixed broken \ref CONTACTMAP with SUM
-- Fixed \ref DUMPATOMS with gro file and more than 100k atoms.
-- Added CMDIST in \ref CONTACTMAP to emulate plumed1 CMAP.
+- Fixed bug in [CENTER](CENTER.md) where default WEIGHTS were missing. 
+- Fixed broken [CONTACTMAP](CONTACTMAP.md) with SUM
+- Fixed [DUMPATOMS](DUMPATOMS.md) with gro file and more than 100k atoms.
+- Added CMDIST in [CONTACTMAP](CONTACTMAP.md) to emulate plumed1 CMAP.
 - Several small fixes in documentation and log file.
 
-For developers:
+### For developers:
+
 - Fixed cmd("getBias") to retrieve bias. It was not working with
   single precision codes and it was not converting units properly.
 - Fixed a regression in 2.0.2 concerning include files from installed plumed
@@ -127,36 +131,42 @@ For developers:
 Version 2.0.4 (September 15, 2014)
 ----------------------------------------------
 
-For users:
-- Fixed a bug in \ref BIASVALUE that could produce wrong acceptance with replica exchange simulations.
+### For users:
+
+- Fixed a bug in [BIASVALUE](BIASVALUE.md) that could produce wrong acceptance with replica exchange simulations.
 - Fixed a few innocuous memory leaks.
 - Fixed reader for xyz files, that now correctly detects missing columns. Also a related regtest has
   been changed.
 - Several small fixes in documentation and log file.
 
-For developers:
+### For developers:
+
 - Renamed Value.cpp to BiasValue.cpp
 
 Version 2.0.5 (December 15, 2014)
 ----------------------------------------------
 
-\plumednotmaintained
+!!! warning "Not maintained"
+
+    This branch is not maintained Users are invited to upgrade to a newer version.
+
+### For users:
 
-For users:
 - Fixed a bug in replica exchange with different Hamiltonians (either lambda-dynamics
   or plumed XX-hrex branch) possibly occurring when using charge or mass dependent
   variables.
-- Fixed a bug in analysis (e.g. \ref HISTOGRAM) leading to wrong accumulation
+- Fixed a bug in analysis (e.g. [HISTOGRAM](HISTOGRAM.md)) leading to wrong accumulation
   of statistics when running a replica exchange simulation.
 - Fixed a bug in the calculation of derivatives in histograms. This should
   be harmless since people usually only consider the value in histograms
   and not the derivatives.
 - Fixed an issue in Makefile that could results in problems when
-  patching an MD code with --shared option (pointed out by Abhi Acharya).
+  patching an MD code with `--shared` option (pointed out by Abhi Acharya).
   This fixes a regression introduced in 2.0.2.
 - Small fixes in documentation.
 
-For developers:
+### For developers:
+
 - Added warning when performing regtests using an instance of plumed from
   a different directory