Reference manual: Show modularized sagelib packages separately

build/bin/sage-spkg-info

@@ -9,7 +9,7 @@ PKG_SCRIPTS="$SAGE_ROOT/build/pkgs/$PKG_BASE"
 for ext in rst txt; do
     SPKG_FILE="$PKG_SCRIPTS/SPKG.$ext"
     if [ -f "$SPKG_FILE" ]; then
-        cat "$SPKG_FILE"
+        sed "1,3s/^ *Sage: Open Source Mathematics Software:/$PKG_BASE:/" "$SPKG_FILE"
         break
     fi
 done

src/doc/bootstrap

@@ -89,8 +89,8 @@ fi
 OUTPUT_INDEX="$OUTPUT_DIR"/index.rst
 cat > "$OUTPUT_INDEX" <<EOF
 
-External Packages
-=================
+Features, Distributions, and External Packages
+==============================================
 
 Standard Packages
 -----------------
@@ -100,7 +100,16 @@ Sage depends.  It installs them automatically if it does not find
 equivalent system packages.
 
 EOF
-for PKG_BASE in $(sage-package list --has-file SPKG.rst :standard: | sort); do
+for PKG_BASE in $(sage-package list --has-file SPKG.rst :standard: | grep -v '^sagemath_' | sort); do
+    echo "* :ref:\`spkg_$PKG_BASE\`"
+done >> "$OUTPUT_INDEX"
+cat >> "$OUTPUT_INDEX" <<EOF
+
+Packages of the Modularized Sage Library
+----------------------------------------
+
+EOF
+for PKG_BASE in $(sage-package list --has-file SPKG.rst | grep '^sagemath_' | sort); do
     echo "* :ref:\`spkg_$PKG_BASE\`"
 done >> "$OUTPUT_INDEX"
 cat >> "$OUTPUT_INDEX" <<EOF
@@ -112,7 +121,7 @@ For additional functionality, you can install some of the following
 optional packages.
 
 EOF
-for PKG_BASE in $(sage-package list --has-file SPKG.rst :optional: | sort); do
+for PKG_BASE in $(sage-package list --has-file SPKG.rst :optional: | grep -v '^sagemath_' | sort); do
     echo "* :ref:\`spkg_$PKG_BASE\`"
 done >> "$OUTPUT_INDEX"
 cat >> "$OUTPUT_INDEX" <<EOF
@@ -125,11 +134,48 @@ Some packages that provide additional functionality are marked as
 integration of these packages into the Sage distribution.
 
 EOF
-for PKG_BASE in $(sage-package list --has-file SPKG.rst :experimental: | sort); do
+for PKG_BASE in $(sage-package list --has-file SPKG.rst :experimental: | grep -v '^sagemath_' | sort); do
     echo "* :ref:\`spkg_$PKG_BASE\`"
 done >> "$OUTPUT_INDEX"
 cat >> "$OUTPUT_INDEX" <<EOF
 
+Runtime-Detectable Features and Conditional Doctests
+----------------------------------------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   sage/features
+   sage/features/sagemath
+   sage/features/pkg_systems
+   sage/features/bliss
+   sage/features/csdp
+   sage/features/databases
+   sage/features/dvipng
+   sage/features/ffmpeg
+   sage/features/four_ti_2
+   sage/features/gap
+   sage/features/graph_generators
+   sage/features/graphviz
+   sage/features/imagemagick
+   sage/features/interfaces
+   sage/features/internet
+   sage/features/kenzo
+   sage/features/latex
+   sage/features/latte
+   sage/features/lrs
+   sage/features/mcqd
+   sage/features/meataxe
+   sage/features/mip_backends
+   sage/features/normaliz
+   sage/features/pandoc
+   sage/features/pdf2svg
+   sage/features/polymake
+   sage/features/rubiks
+   sage/features/tdlib
+   sage/features/join_feature
+   sage/features/all
+
 All External Packages
 ---------------------
 
@@ -142,11 +188,14 @@ EOF
 
 OUTPUT_INDEX="$OUTPUT_DIR"/index_alph.rst
 cat >> "$OUTPUT_INDEX" <<EOF
+
 Details of external packages
 ============================
 
 Packages are in alphabetical order.
 
+.. default-role:: code
+
 .. toctree::
    :maxdepth: 1
 
@@ -160,3 +209,8 @@ for PKG_BASE in $(sage-package list --has-file SPKG.rst | sort); do
             (echo ".. _spkg_$PKG_BASE:" && echo && OUTPUT_RST=1 sage-spkg-info $PKG_BASE) | sed -e "s|https://github.com/sagemath/sage/issues/\([0-9]*\)|:issue:\`\1\`|g" -e "s|https://arxiv.org/abs/cs/\([0-9]*\)|:arxiv:\`cs/\1\`|g" > "$OUTPUT_DIR"/$PKG_BASE.rst
             echo >> "$OUTPUT_INDEX" "   $PKG_BASE"
 done
+cat >> "$OUTPUT_INDEX" <<EOF
+
+.. default-role::
+
+EOF

src/doc/en/reference/misc/index.rst

@@ -141,44 +141,6 @@ Fast Expression Evaluation
 ..   sage/ext/interpreters/wrapper_rdf
 ..   sage/ext/interpreters/wrapper_rr
 
-Features
-~~~~~~~~
-
-.. toctree::
-   :maxdepth: 1
-
-   sage/features
-   sage/features/join_feature
-   sage/features/all
-   sage/features/sagemath
-   sage/features/pkg_systems
-   sage/features/bliss
-   sage/features/csdp
-   sage/features/databases
-   sage/features/dvipng
-   sage/features/ffmpeg
-   sage/features/four_ti_2
-   sage/features/gap
-   sage/features/graph_generators
-   sage/features/graphviz
-   sage/features/imagemagick
-   sage/features/interfaces
-   sage/features/internet
-   sage/features/kenzo
-   sage/features/latex
-   sage/features/latte
-   sage/features/lrs
-   sage/features/mcqd
-   sage/features/meataxe
-   sage/features/mip_backends
-   sage/features/normaliz
-   sage/features/pandoc
-   sage/features/pdf2svg
-   sage/features/polymake
-   sage/features/rubiks
-   sage/features/tdlib
-
-
 Code Evaluation
 ---------------
 

src/sage/features/bliss.py

@@ -35,7 +35,7 @@
 
 class BlissLibrary(CythonFeature):
     r"""
-    A :class:`~sage.features.Feature` which describes whether the Bliss library is
+    A :class:`~sage.features.Feature` which describes whether the :ref:`Bliss library <spkg_bliss>` is
     present and functional.
 
     EXAMPLES::

src/sage/features/cddlib.py

@@ -17,7 +17,7 @@
 class CddExecutable(Executable):
     r"""
     A :class:`~sage.features.Feature` describing the presence of an executable
-    which comes as a part of ``cddlib``.
+    which comes as a part of :ref:`cddlib <spkg_cddlib>`.
 
     EXAMPLES::
 

src/sage/features/csdp.py

@@ -25,7 +25,7 @@
 class CSDP(Executable):
     r"""
     A :class:`~sage.features.Feature` which checks for the ``theta`` binary
-    of CSDP.
+    of :ref:`CSDP <spkg_csdp>`.
 
     EXAMPLES::
 

src/sage/features/databases.py

@@ -26,8 +26,8 @@
 
 class DatabaseConwayPolynomials(StaticFile):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of Frank Luebeck's
-    database of Conway polynomials.
+    A :class:`~sage.features.Feature` which describes the presence of :ref:`Frank Luebeck's
+    database of Conway polynomials <spkg_conway_polynomials>`.
 
     EXAMPLES::
 
@@ -60,8 +60,8 @@ def __init__(self):
 
 class DatabaseCremona(StaticFile):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of John Cremona's
-    database of elliptic curves.
+    A :class:`~sage.features.Feature` which describes the presence of :ref:`John Cremona's
+    database of elliptic curves <spkg_database_cremona_ellcurve>`.
 
     INPUT:
 
@@ -73,7 +73,7 @@ class DatabaseCremona(StaticFile):
         sage: from sage.features.databases import DatabaseCremona
         sage: DatabaseCremona('cremona_mini').is_present()
         FeatureTestResult('database_cremona_mini_ellcurve', True)
-        sage: DatabaseCremona().is_present()  # optional - database_cremona_ellcurve
+        sage: DatabaseCremona().is_present()                                    # optional - database_cremona_ellcurve
         FeatureTestResult('database_cremona_ellcurve', True)
     """
     def __init__(self, name="cremona", spkg="database_cremona_ellcurve"):
@@ -94,7 +94,8 @@ def __init__(self, name="cremona", spkg="database_cremona_ellcurve"):
 
 class DatabaseJones(StaticFile):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of John Jones's tables of number fields.
+    A :class:`~sage.features.Feature` which describes the presence of
+    :ref:`John Jones's tables of number fields <spkg_database_jones_numfield>`.
 
     EXAMPLES::
 
@@ -118,12 +119,13 @@ def __init__(self):
 
 class DatabaseKnotInfo(PythonModule):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of the databases at the
+    A :class:`~sage.features.Feature` which describes the presence of the
+    :ref:`package providing the KnotInfo and LinkInfo databases <spkg_database_knotinfo>`.
+
+    The homes of these databases are the
     web-pages `KnotInfo <https://knotinfo.math.indiana.edu/>`__ and
     `LinkInfo <https://linkinfo.sitehost.iu.edu>`__.
 
-
-
     EXAMPLES::
 
         sage: from sage.features.databases import DatabaseKnotInfo
@@ -140,9 +142,13 @@ def __init__(self):
         """
         PythonModule.__init__(self, 'database_knotinfo', spkg='database_knotinfo')
 
+
 class DatabaseCubicHecke(PythonModule):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of the databases at the
+    A :class:`~sage.features.Feature` which describes the presence of the
+    :ref:`Cubic Hecke algebra database package <spkg_database_cubic_hecke>`.
+
+    The home of this database is the
     web-page `Cubic Hecke algebra on 4 strands <http://www.lamfa.u-picardie.fr/marin/representationH4-en.html>`__
     of Ivan Marin.
 
@@ -162,10 +168,12 @@ def __init__(self):
         """
         PythonModule.__init__(self, 'database_cubic_hecke', spkg='database_cubic_hecke')
 
+
 class DatabaseReflexivePolytopes(StaticFile):
     r"""
-    A :class:`~sage.features.Feature` which describes the presence of the PALP database
-    of reflexive lattice polytopes.
+    A :class:`~sage.features.Feature` which describes the presence of the
+    :ref:`PALP databases of reflexive three-dimensional <spkg_polytopes_db>`
+    and :ref:`four-dimensional lattice polytopes <spkg_polytopes_db_4d>`.
 
     EXAMPLES::
 

src/sage/features/ffmpeg.py

@@ -15,7 +15,7 @@
 
 class FFmpeg(Executable):
     r"""
-    A :class:`~sage.features.Feature` describing the presence of ``ffmpeg``
+    A :class:`~sage.features.Feature` describing the presence of :ref:`ffmpeg <spkg_ffmpeg>`.
 
     EXAMPLES::
 

src/sage/features/four_ti_2.py

@@ -8,7 +8,7 @@
 
 class FourTi2Executable(Executable):
     r"""
-    A :class:`~sage.features.Feature` for the 4ti2 executables.
+    A :class:`~sage.features.Feature` for the :ref:`4ti2 <spkg_4ti2>` executables.
     """
     def __init__(self, name):
         r"""
@@ -27,7 +27,7 @@ def __init__(self, name):
 
 class FourTi2(JoinFeature):
     r"""
-    A :class:`~sage.features.Feature` describing the presence of the ``4ti2`` executables.
+    A :class:`~sage.features.Feature` describing the presence of all :ref:`4ti2 <spkg_4ti2>` executables.
 
     EXAMPLES::
 

src/sage/features/gap.py

@@ -1,5 +1,5 @@
 r"""
-Features for testing the presence of GAP packages
+Features for testing the presence of the SageMath interfaces to ``gap`` and of GAP packages
 """
 # *****************************************************************************
 #       Copyright (C) 2016 Julian Rüth
@@ -62,7 +62,7 @@ def _is_present(self):
 class sage__libs__gap(JoinFeature):
     r"""
     A :class:`sage.features.Feature` describing the presence of :mod:`sage.libs.gap`
-    (the library interface to GAP) and :mod:`sage.interfaces.gap` (the pexpect
+    (the library interface to :ref:`GAP <spkg_gap>`) and :mod:`sage.interfaces.gap` (the pexpect
     interface to GAP). By design, we do not distinguish between these two, in order
     to facilitate the conversion of code from the pexpect interface to the library
     interface.

src/sage/features/gfan.py

@@ -16,7 +16,7 @@
 
 class GfanExecutable(Executable):
     r"""
-    A :class:`~sage.features.Feature` for the gfan executables.
+    A :class:`~sage.features.Feature` for the :ref:`gfan <spkg_gfan>` executables.
     """
     def __init__(self, cmd=None):
         r"""

src/sage/features/graph_generators.py

@@ -1,5 +1,5 @@
 r"""
-Features for testing the presence of various graph generator programs
+Features for testing the presence of graph generator programs ``benzene``, ``buckygen``, ``plantri``
 """
 
 # *****************************************************************************
@@ -23,7 +23,7 @@
 
 class Plantri(Executable):
     r"""
-    A :class:`~sage.features.Feature` which checks for the ``plantri`` binary.
+    A :class:`~sage.features.Feature` which checks for the :ref:`plantri <spkg_plantri>` binary.
 
     EXAMPLES::
 
@@ -70,7 +70,7 @@ def is_functional(self):
 
 class Buckygen(Executable):
     r"""
-    A :class:`~sage.features.Feature` which checks for the ``buckygen`` binary.
+    A :class:`~sage.features.Feature` which checks for the :ref:`buckygen <spkg_buckygen>` binary.
 
     EXAMPLES::
 
@@ -117,7 +117,7 @@ def is_functional(self):
 
 class Benzene(Executable):
     r"""
-    A :class:`~sage.features.Feature` which checks for the ``benzene``
+    A :class:`~sage.features.Feature` which checks for the :ref:`benzene <spkg_benzene>`
     binary.
 
     EXAMPLES::