30352: installation via PyPI

Author: soehms

build/pkgs/database_knotinfo/SPKG.rst

@@ -1,57 +1,18 @@
-database_knotinfo: Tables of Knots and Links from the KnotInfo Databases
-========================================================================
+database_knotinfo: Content of the KnotInfo and LinkInfo databases as lists of dictionaries
+==========================================================================================
 
 Description
 -----------
 
-Database for named knots and links provided at
+Content of the KnotInfo and LinkInfo databases as lists of dictionaries
 
-https://knotinfo.math.indiana.edu/
-
-and
-
-https://linkinfo.sitehost.iu.edu'
-
-Dependencies
-------------
-
-- Sage library
+License
+-------
 
+GPL
 
 Upstream Contact
 ----------------
 
-- Charles Livingston <[email protected]>
-- Allison H. Moore <[email protected]>
-
-Update Instructions
--------------------
-
-- See the Python script ``create_knotinfo_tarball.py`` in the current directory.
-
-Changelog
----------
-
-- 20200713 (Sebastian Oehms, 13 Juli 2020, :trac:`30352`, initial version)
-
-  The tarball has been created from the both download files at the
-  given date:
-
-  ``knotinfo_data_complete.xls``
-  ``linkinfo_data_complete.xlsx``
-
-  exporting them to CSV via LibreOffice.
-
-  The second file has been changed manually deleting one character:
-  a trailing "}" occuring in the homfly_polynomial column of the last
-  link ``L11n459{1,1,1}``.
-
-- 20210201 (Sebastian Oehms, 1 February 2021, :trac:`30352`, upgrade)
-
-  Three new columns have been added to ``knotinfo_data_complete.xls``
-  (``montesinos_notation``, ``boundary_slopes`` and ``pretzel_notation``).
-  ``linkinfo_data_complete.xlsx`` remains unchanged.
+https://pypi.org/project/database-knotinfo/
 
-  The tarball has been created using ``create_knotinfo_tarball.py``.
-  The fix concerning the misplaced character for ``L11n459{1,1,1}``
-  is performed in :meth:`KnotInfoBase.homfly_polynomial`, now.

build/pkgs/database_knotinfo/checksums.ini

@@ -1,5 +1,5 @@
-tarball=knotinfo-20210201.tar.bz2
-sha1=a8a69dacd1f61f19a921d8e5b90d6cfdea85d859
-md5=5f53bd7e3a672648d41460c4d22d52b3
-cksum=1608275975
-upstream_url=https://github.com/soehms/sagemath_knotinfo/blob/main/knotinfo-20210201.tar.bz2?raw=true
+tarball=database_knotinfo-VERSION.tar.gz
+sha1=2d758c5f8bf346162d13bec1d5bccfec9d27baa1
+md5=ec20d43af0c4ecf59dfd281c6ccc4ef0
+cksum=2792610748
+upstream_url=https://pypi.io/packages/source/d/database_knotinfo/database_knotinfo-VERSION.tar.gz

build/pkgs/database_knotinfo/create_knotinfo_tarball.py

@@ -1,5 +1,4 @@
-| $(SAGERUNTIME)
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.
-It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/database_knotinfo/dependencies

@@ -0,0 +1 @@
+database-knotinfo

build/pkgs/database_knotinfo/install-requires.txt

@@ -1 +1 @@
-20210201
+0.7

build/pkgs/database_knotinfo/package-version.txt

@@ -1,21 +1,9 @@
-INSTALL="yes"
-TARGET="${SAGE_SHARE}/knotinfo"
-VERSION=`cat package-version.txt`
-if [ -d $TARGET ]
-then
-    diff package-version.txt $TARGET > /dev/null 2>&1
-    if [ $? -eq 0 ]
-    then
-        INSTALL="no"
-        echo "Version $VERSION of knotinfo already installed"
-    else
-        OLD_VERSION=`cat $TARGET/package-version.txt`
-        echo "Removing former version $OLD_VERSION of knotinfo"
-        rm -rf $TARGET
-    fi
-fi
+cd src
+sdh_pip_install .
 
-if [ "$INSTALL" = "yes" ]
+FILECACHE="${SAGE_SHARE}/knotinfo"
+if [ -d $FILECACHE ]
 then
-    exec python3 spkg-install.py
+    echo "Clearing former filecache of knotinfo"
+    rm -rf $FILECACHE
 fi

build/pkgs/database_knotinfo/spkg-install.in

@@ -26,7 +26,6 @@
 
 
 import os
-import csv
 from enum import Enum
 
 from sage.structure.sage_object import SageObject
@@ -227,6 +226,20 @@ def csv(self):
         """
         return '%s.csv' %(self.value[1])
 
+    def num_knots(self):
+        r"""
+        Return the file name under which the number of knots is stored
+        in an sobj-file.
+
+        Examples::
+
+            sage: from sage.databases.knotinfo_db import KnotInfoDataBase
+            sage: ki_db = KnotInfoDataBase()
+            sage: ki_db.filename.knots.num_knots()
+            'num_knots.sobj'
+        """
+        return 'num_knots.sobj'
+
     def sobj_row(self):
         r"""
         Return the file name under which the row-data of the csv-File
@@ -347,10 +360,9 @@ def __init__(self, install=False):
                                       'linkinfo_data_complete']>
         """
         # some constants
-        self._delimiter    = '|'
-        self._names_column = 'name'
+        self._names_column      = 'name'
         self._components_column = 'components'
-        self._knot_prefix  = 'K'
+        self._knot_prefix       = 'K'
 
         self._knot_list = None
         self._link_list = None
@@ -359,16 +371,34 @@ def __init__(self, install=False):
 
         from sage.features.databases import DatabaseKnotInfo
         self._feature   = DatabaseKnotInfo()
-        self._sobj_path = self._feature.search_path[0]
+        self._sobj_path = self._feature._sobj_path
+
+    def reset_filecache(self):
+        r"""
+        Reset the internal files containing the database.
+
+        EXAMPLES::
+
+            sage: from sage.databases.knotinfo_db import KnotInfoDataBase
+            sage: ki_db = KnotInfoDataBase()
+            sage: ki_db.reset_filecache()    # optional - database_knotinfo
+        """
+        if not self._feature.is_present():
+            return
+        sobj_path = self._sobj_path
+        os.system('rm -rf %s' %sobj_path)
+        from sage.misc.misc import sage_makedirs
+        sage_makedirs(sobj_path)
+
+        num_knots_file = os.path.join(sobj_path, self.filename.knots.num_knots())
+        knot_list = self.knot_list()
+        num_knots = len(knot_list) - 1
+        save(num_knots, num_knots_file)
+        self._num_knots = num_knots
+        self._create_col_dict_sobj()
+        self._create_data_sobj()
+        return
 
-        if install:
-            knot_list = self.knot_list()
-            num_knots = len(knot_list) - 1
-            print('Setting the number of Knots: %s!' %num_knots)
-            save(num_knots, '%s/%s' %(self._sobj_path, self._feature.filename))
-            self._feature._cache_is_present = None # must be reset for package installation
-            self._create_col_dict_sobj()
-            self._create_data_sobj()
 
     def demo_version(self):
         r"""
@@ -382,9 +412,14 @@ def demo_version(self):
             sage: ki_db.demo_version()       # optional - database_knotinfo
             False
         """
-        if not self._demo:
+        if self._demo is None:
             if self._feature.is_present():
-                self._num_knots =  load(self._feature.absolute_path())
+                num_knots_file = os.path.join(self._sobj_path, self.filename.knots.num_knots())
+                from builtins import FileNotFoundError
+                try:
+                    self._num_knots =  load(num_knots_file)
+                except FileNotFoundError:
+                    self.reset_filecache()
                 self._demo = False
             else:
                 self._demo = True
@@ -404,12 +439,8 @@ def knot_list(self):
         if self._knot_list:
             return self._knot_list
 
-        print('Importing KnotInfo database from SPKG!')
-        os.system('pwd')
-        knot_csv = open('src/%s' %self.filename.knots.csv())
-        knot_dict = csv.DictReader(knot_csv, delimiter=self._delimiter)
-        self._knot_list = list(knot_dict)
-        knot_csv.close()
+        from database_knotinfo import link_list
+        self._knot_list = link_list()
         return self._knot_list
 
 
@@ -426,11 +457,8 @@ def link_list(self):
         if self._link_list:
             return self._link_list
 
-        print('Importing LinkInfo database from SPKG!')
-        link_csv = open('src/%s' %self.filename.links.csv())
-        link_dict = csv.DictReader(link_csv, delimiter=self._delimiter)
-        self._link_list = list(link_dict)
-        link_csv.close()
+        from database_knotinfo import link_list
+        self._link_list = link_list(proper_links=True)
         return self._link_list
 
     def _create_col_dict_sobj(self):
@@ -786,6 +814,7 @@ def _test_database(self, **options):
 db = KnotInfoDataBase()
 dc = db.columns()
 
+
 data_demo_sample = {
     dc.name: ['0_1', '3_1', '4_1', '5_1', '5_2', '6_1', '6_2', '6_3', '7_1', '7_2',
               'L2a1{0}', 'L2a1{1}', 'L4a1{0}', 'L4a1{1}', 'L5a1{0}', 'L5a1{1}',