Unverified Commit 6b79b1f9 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

use table_from_list in Packages_details and check for completenes there, too

parent b1757bb2

doc/src/Packages_details.rst

+81 −30
Original line number Diff line number Diff line
@@ -26,35 +26,86 @@ page gives those details. 


.. _lc: Commands_all.html



+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`ASPHERE <PKG-ASPHERE>` | :ref:`BODY <PKG-BODY>`         | :ref:`CLASS2 <PKG-CLASS2>`     | :ref:`COLLOID <PKG-COLLOID>` | :ref:`COMPRESS <PKG-COMPRESS>` | :ref:`CORESHELL <PKG-CORESHELL>` |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`DIPOLE <PKG-DIPOLE>`   | :ref:`GPU <PKG-GPU>`           | :ref:`GRANULAR <PKG-GRANULAR>` | :ref:`KIM <PKG-KIM>`         | :ref:`KOKKOS <PKG-KOKKOS>`     | :ref:`KSPACE <PKG-KSPACE>`       |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`LATTE <PKG-LATTE>`     | :ref:`MANYBODY <PKG-MANYBODY>` | :ref:`MC <PKG-MC>`             | :ref:`MESSAGE <PKG-MESSAGE>` | :ref:`MISC <PKG-MISC>`         | :ref:`MOLECULE <PKG-MOLECULE>`   |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`MPIIO <PKG-MPIIO>`     | :ref:`MSCG <PKG-MSCG>`         | :ref:`OPT <PKG-OPT>`           | :ref:`PERI <PKG-PERI>`       | :ref:`POEMS <PKG-POEMS>`       | :ref:`PYTHON <PKG-PYTHON>`       |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`QEQ <PKG-QEQ>`         | :ref:`REPLICA <PKG-REPLICA2>`  | :ref:`RIGID <PKG-RIGID>`       | :ref:`SHOCK <PKG-SHOCK>`     | :ref:`SNAP <PKG-SNAP>`         | :ref:`SPIN <PKG-SPIN>`           |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+

| :ref:`SRD <PKG-SRD>`         | :ref:`VORONOI <PKG-VORONOI>`   |                                |                              |                                |                                  |

+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+



+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-ADIOS <PKG-USER-ADIOS>`     | :ref:`USER-ATC <PKG-USER-ATC>`                 | :ref:`USER-AWPMD <PKG-USER-AWPMD>` | :ref:`USER-BOCS <PKG-USER-BOCS>`         | :ref:`USER-CGDNA <PKG-USER-CGDNA>`   | :ref:`USER-CGSDK <PKG-USER-CGSDK>` |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | :ref:`USER-DPD <PKG-USER-DPD>`     | :ref:`USER-DRUDE <PKG-USER-DRUDE>`       | :ref:`USER-EFF <PKG-USER-EFF>`       | :ref:`USER-FEP <PKG-USER-FEP>`     |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-H5MD <PKG-USER-H5MD>`       | :ref:`USER-INTEL <PKG-USER-INTEL>`             | :ref:`USER-LB <PKG-USER-LB>`       | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | :ref:`USER-MEAMC <PKG-USER-MEAMC>`   | :ref:`USER-MESO <PKG-USER-MESO>`   |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-MGPT <PKG-USER-MGPT>`       | :ref:`USER-MISC <PKG-USER-MISC>`               | :ref:`USER-MOFFF <PKG-USER-MOFFF>` | :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`   | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | :ref:`USER-OMP <PKG-USER-OMP>`     |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-PHONON <PKG-USER-PHONON>`   | :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`USER-PTM <PKG-USER-PTM>`     | :ref:`USER-QMMM <PKG-USER-QMMM>`         | :ref:`USER-QTB <PKG-USER-QTB>`       | :ref:`USER-QUIP <PKG-USER-QUIP>`   |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-REAXC <PKG-USER-REAXC>`     | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`       | :ref:`USER-SDPD <PKG-USER-SDPD>`   | :ref:`USER-SMD <PKG-USER-SMD>`           | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`   | :ref:`USER-SPH <PKG-USER-SPH>`     |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

| :ref:`USER-TALLY <PKG-USER-TALLY>`     | :ref:`USER-UEF <PKG-USER-UEF>`                 | :ref:`USER-VTK <PKG-USER-VTK>`     | :ref:`USER-YAFF <PKG-USER-YAFF>`         |                                      |                                    |

+----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+

.. table_from_list::

   :columns: 6



   * :ref:`ASPHERE <PKG-ASPHERE>`

   * :ref:`BODY <PKG-BODY>`

   * :ref:`CLASS2 <PKG-CLASS2>`

   * :ref:`COLLOID <PKG-COLLOID>`

   * :ref:`COMPRESS <PKG-COMPRESS>`

   * :ref:`CORESHELL <PKG-CORESHELL>`

   * :ref:`DIPOLE <PKG-DIPOLE>`

   * :ref:`GPU <PKG-GPU>`

   * :ref:`GRANULAR <PKG-GRANULAR>`

   * :ref:`KIM <PKG-KIM>`

   * :ref:`KOKKOS <PKG-KOKKOS>`

   * :ref:`KSPACE <PKG-KSPACE>`

   * :ref:`LATTE <PKG-LATTE>`

   * :ref:`MANYBODY <PKG-MANYBODY>`

   * :ref:`MC <PKG-MC>`

   * :ref:`MESSAGE <PKG-MESSAGE>`

   * :ref:`MISC <PKG-MISC>`

   * :ref:`MOLECULE <PKG-MOLECULE>`

   * :ref:`MPIIO <PKG-MPIIO>`

   * :ref:`MSCG <PKG-MSCG>`

   * :ref:`OPT <PKG-OPT>`

   * :ref:`PERI <PKG-PERI>`

   * :ref:`POEMS <PKG-POEMS>`

   * :ref:`PYTHON <PKG-PYTHON>`

   * :ref:`QEQ <PKG-QEQ>`

   * :ref:`REPLICA <PKG-REPLICA>`

   * :ref:`RIGID <PKG-RIGID>`

   * :ref:`SHOCK <PKG-SHOCK>`

   * :ref:`SNAP <PKG-SNAP>`

   * :ref:`SPIN <PKG-SPIN>`

   * :ref:`SRD <PKG-SRD>`

   * :ref:`VORONOI <PKG-VORONOI>`





.. table_from_list::

   :columns: 6



   * :ref:`USER-ADIOS <PKG-USER-ADIOS>`

   * :ref:`USER-ATC <PKG-USER-ATC>`

   * :ref:`USER-AWPMD <PKG-USER-AWPMD>`

   * :ref:`USER-BOCS <PKG-USER-BOCS>`

   * :ref:`USER-CGDNA <PKG-USER-CGDNA>`

   * :ref:`USER-CGSDK <PKG-USER-CGSDK>`

   * :ref:`USER-COLVARS <PKG-USER-COLVARS>`

   * :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>`

   * :ref:`USER-DPD <PKG-USER-DPD>`

   * :ref:`USER-DRUDE <PKG-USER-DRUDE>`

   * :ref:`USER-EFF <PKG-USER-EFF>`

   * :ref:`USER-FEP <PKG-USER-FEP>`

   * :ref:`USER-H5MD <PKG-USER-H5MD>`

   * :ref:`USER-INTEL <PKG-USER-INTEL>`

   * :ref:`USER-LB <PKG-USER-LB>`

   * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`

   * :ref:`USER-MEAMC <PKG-USER-MEAMC>`

   * :ref:`USER-MESO <PKG-USER-MESO>`

   * :ref:`USER-MGPT <PKG-USER-MGPT>`

   * :ref:`USER-MISC <PKG-USER-MISC>`

   * :ref:`USER-MOFFF <PKG-USER-MOFFF>`

   * :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`

   * :ref:`USER-NETCDF <PKG-USER-NETCDF>`

   * :ref:`USER-OMP <PKG-USER-OMP>`

   * :ref:`USER-PHONON <PKG-USER-PHONON>`

   * :ref:`USER-PLUMED <PKG-USER-PLUMED>`

   * :ref:`USER-PTM <PKG-USER-PTM>`

   * :ref:`USER-QMMM <PKG-USER-QMMM>`

   * :ref:`USER-QTB <PKG-USER-QTB>`

   * :ref:`USER-QUIP <PKG-USER-QUIP>`

   * :ref:`USER-REAXC <PKG-USER-REAXC>`

   * :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`

   * :ref:`USER-SDPD <PKG-USER-SDPD>`

   * :ref:`USER-SMD <PKG-USER-SMD>`

   * :ref:`USER-SMTBQ <PKG-USER-SMTBQ>`

   * :ref:`USER-SPH <PKG-USER-SPH>`

   * :ref:`USER-TALLY <PKG-USER-TALLY>`

   * :ref:`USER-UEF <PKG-USER-UEF>`

   * :ref:`USER-VTK <PKG-USER-VTK>`

   * :ref:`USER-YAFF <PKG-USER-YAFF>`





----------
@@ -880,7 +931,7 @@ part of their formulation. 
----------





.. _PKG-REPLICA2:

.. _PKG-REPLICA:



REPLICA package

---------------

doc/src/Packages_standard.rst

+1 −1
Original line number Diff line number Diff line
@@ -75,7 +75,7 @@ package: 
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

| :ref:`QEQ <PKG-QEQ>`             | QEq charge equilibration             | :doc:`fix qeq <fix_qeq>`                           | qeq                                                 | no      |

+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

| :ref:`REPLICA <PKG-REPLICA2>`    | multi-replica methods                | :doc:`Howto replica <Howto_replica>`               | tad                                                 | no      |

| :ref:`REPLICA <PKG-REPLICA>`     | multi-replica methods                | :doc:`Howto replica <Howto_replica>`               | tad                                                 | no      |

+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

| :ref:`RIGID <PKG-RIGID>`         | rigid bodies and constraints         | :doc:`fix rigid <fix_rigid>`                       | rigid                                               | no      |

+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

doc/utils/check-packages.py

+16 −0
Original line number Diff line number Diff line
@@ -76,6 +76,22 @@ for p in usrpkg: 
    print("User package %s missing in Packages_user.rst"

          % p)



fp = open(os.path.join(doc,'Packages_details.rst'))

text = fp.read()

fp.close()

matches = re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)

for p in stdpkg:

  if not p in matches:

    ++counter

    print("Standard package %s missing in Packages_details.rst"

          % p)

matches = re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)

for p in usrpkg:

  if not p in matches:

    ++counter

    print("User package %s missing in Packages_details.rst"

          % p)



if counter:

    print("Found %d issue(s) with package lists" % counter)

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