From a699113e1575e0379736228734d6ae6c43f4edb6 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Sat, 9 Nov 2024 18:14:25 +0700
Subject: [PATCH 01/11] Allow passing view_annotate=True to Cython compilation

---
 src/sage/misc/cython.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index c542e0d1919..01f3d7f580d 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -24,6 +24,7 @@
 import re
 import sys
 import shutil
+import webbrowser
 
 from sage.env import (SAGE_LOCAL, cython_aliases,
                       sage_include_directories)
@@ -79,8 +80,8 @@ def _standard_libs_libdirs_incdirs_aliases():
 
 
 def cython(filename, verbose=0, compile_message=False,
-           use_cache=False, create_local_c_file=False, annotate=True, sage_namespace=True,
-           create_local_so_file=False):
+           use_cache=False, create_local_c_file=False, annotate=True, view_annotate=False,
+           sage_namespace=True, create_local_so_file=False):
     r"""
     Compile a Cython file. This converts a Cython file to a C (or C++ file),
     and then compiles that. The .c file and the .so file are
@@ -110,6 +111,9 @@ def cython(filename, verbose=0, compile_message=False,
       in the temporary directory, but if ``create_local_c_file`` is also True,
       then save a copy of the .html file in the current directory.
 
+    - ``view_annotate`` -- boolean (default: ``False``); if ``True``, open the
+      annotated html file in a web browser using :func:`webbrowser.open`
+
     - ``sage_namespace`` -- boolean (default: ``True``); if ``True``, import
       ``sage.all``
 
@@ -392,6 +396,11 @@ def cython(filename, verbose=0, compile_message=False,
             shutil.copy(os.path.join(target_dir, name + ".html"),
                         os.curdir)
 
+    if view_annotate:
+        if not annotate:
+            raise ValueError("Cannot view annotated file without creating it")
+        webbrowser.open(os.path.join(target_dir, name + ".html"))
+
     # This emulates running "setup.py build" with the correct options
     #
     # setuptools plugins considered harmful:

From 64890af2100c4b36df1edd54c919382b34a2eaf7 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Sun, 10 Nov 2024 18:19:54 +0700
Subject: [PATCH 02/11] Add tests for view_annotate

---
 src/sage/misc/cython.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index 01f3d7f580d..3016167c0be 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -241,6 +241,23 @@ def cython(filename, verbose=0, compile_message=False,
         RuntimeError: Error compiling Cython file:
         ...
         ...: 'sage/misc.pxd' not found
+
+    Test ``view_annotate``::
+
+        sage: cython('''
+        ....: def f(int n):
+        ....:     return n*n
+        ....: ''', view_annotate=True)  # optional -- webbrowser
+
+    ::
+
+        sage: cython('''
+        ....: def f(int n):
+        ....:     return n*n
+        ....: ''', view_annotate=True, annotate=False)
+        Traceback (most recent call last):
+        ...
+        ValueError: Cannot view annotated file without creating it
     """
     if not filename.endswith('pyx'):
         print("Warning: file (={}) should have extension .pyx".format(filename), file=sys.stderr)

From 0f386e9fff4a4ce2e649fda912b8e1b27656bd9e Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Thu, 14 Nov 2024 21:42:23 +0700
Subject: [PATCH 03/11] Add view-annotate to IPython magic

---
 src/sage/repl/ipython_extension.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 329a7b9b95a..15a6c0a7edc 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -357,6 +357,7 @@ def cython(self, line, cell):
           - ``--use-cache``
           - ``--create-local-c-file``
           - ``--annotate``
+          - ``--view-annotate``
           - ``--sage-namespace``
           - ``--create-local-so-file``
           - ``--no-compile-message``, ``--no-use-cache``, etc.
@@ -434,6 +435,7 @@ def error(self, message):
         parser.add_argument("--use-cache", action=argparse.BooleanOptionalAction)
         parser.add_argument("--create-local-c-file", action=argparse.BooleanOptionalAction)
         parser.add_argument("--annotate", action=argparse.BooleanOptionalAction)
+        parser.add_argument("--view-annotate", action=argparse.BooleanOptionalAction)
         parser.add_argument("--sage-namespace", action=argparse.BooleanOptionalAction)
         parser.add_argument("--create-local-so-file", action=argparse.BooleanOptionalAction)
         args = parser.parse_args(shlex.split(line))

From f90425dbd93b47eb8cf709ddbdbb1b8ad9161554 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Sat, 7 Dec 2024 23:14:29 +0700
Subject: [PATCH 04/11] Allow view-annotate to display in Sage notebook

---
 src/sage/misc/cython.py            | 21 +++++++++++--
 src/sage/repl/ipython_extension.py | 48 ++++++++++++++++++++++++++++--
 2 files changed, 65 insertions(+), 4 deletions(-)

diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index 3016167c0be..9b3e2428865 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -81,7 +81,7 @@ def _standard_libs_libdirs_incdirs_aliases():
 
 def cython(filename, verbose=0, compile_message=False,
            use_cache=False, create_local_c_file=False, annotate=True, view_annotate=False,
-           sage_namespace=True, create_local_so_file=False):
+           view_annotate_callback=webbrowser.open, sage_namespace=True, create_local_so_file=False):
     r"""
     Compile a Cython file. This converts a Cython file to a C (or C++ file),
     and then compiles that. The .c file and the .so file are
@@ -114,6 +114,11 @@ def cython(filename, verbose=0, compile_message=False,
     - ``view_annotate`` -- boolean (default: ``False``); if ``True``, open the
       annotated html file in a web browser using :func:`webbrowser.open`
 
+    - ``view_annotate_callback`` -- function (default: ``webbrowser.open``); a function
+      that takes a string being the path to the html file. This can be overridden to
+      change what to do with the annotated html file. Have no effect unless
+      ``view_annotate`` is ``True``
+
     - ``sage_namespace`` -- boolean (default: ``True``); if ``True``, import
       ``sage.all``
 
@@ -258,6 +263,18 @@ def cython(filename, verbose=0, compile_message=False,
         Traceback (most recent call last):
         ...
         ValueError: Cannot view annotated file without creating it
+
+    ::
+
+        sage: collected_paths = []
+        sage: cython('''
+        ....: def f(int n):
+        ....:     return n*n
+        ....: ''', view_annotate=True, view_annotate_callback=collected_paths.append)
+        sage: collected_paths
+        ['...']
+        sage: len(collected_paths)
+        1
     """
     if not filename.endswith('pyx'):
         print("Warning: file (={}) should have extension .pyx".format(filename), file=sys.stderr)
@@ -416,7 +433,7 @@ def cython(filename, verbose=0, compile_message=False,
     if view_annotate:
         if not annotate:
             raise ValueError("Cannot view annotated file without creating it")
-        webbrowser.open(os.path.join(target_dir, name + ".html"))
+        view_annotate_callback(os.path.join(target_dir, name + ".html"))
 
     # This emulates running "setup.py build" with the correct options
     #
diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 15a6c0a7edc..34d7d15c36f 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -65,6 +65,8 @@
 """
 
 from IPython.core.magic import Magics, magics_class, line_magic, cell_magic
+from IPython.core.display import HTML
+from IPython import get_ipython
 
 from sage.repl.load import load_wrap
 from sage.env import SAGE_IMPORTALL, SAGE_STARTUP_FILE
@@ -72,6 +74,14 @@
 from sage.misc.misc import run_once
 
 
+def _running_in_notebook():
+    try:
+        from ipykernel.zmqshell import ZMQInteractiveShell
+    except ImportError:
+        return False
+    return isinstance(get_ipython(), ZMQInteractiveShell)
+
+
 @magics_class
 class SageMagics(Magics):
 
@@ -364,6 +374,16 @@ def cython(self, line, cell):
 
           See :func:`~sage.misc.cython.cython` for details.
 
+          For ``--view-annotate``, the following additional choices are allowed:
+
+          - ``--view-annotate=none`` (default)
+          - ``--view-annotate=auto`` (same as ``--view-annotate``); select one of the
+            choices below automatically
+          - ``--view-annotate=webbrowser``; open the annotation in a web browser
+            (preferred if the Sage command line is used)
+          - ``--view-annotate=displayhtml``; display the annotation inline in the notebook
+            (preferred if the Sage notebook is used)
+
         - ``cell`` -- string; the Cython source code to process
 
         OUTPUT: none; the Cython code is compiled and loaded
@@ -404,6 +424,15 @@ def cython(self, line, cell):
             ....: ''')
             UsageError: unrecognized arguments: --help
 
+        Test ``--view-annotate`` invalid arguments::
+
+            sage: # needs sage.misc.cython
+            sage: shell.run_cell('''
+            ....: %%cython --view-annotate=xx
+            ....: print(1)
+            ....: ''')
+            UsageError: argument --view-annotate: invalid choice: 'xx' (choose from 'none', 'auto', 'webbrowser', 'displayhtml')
+
         Test invalid quotes::
 
             sage: # needs sage.misc.cython
@@ -435,11 +464,26 @@ def error(self, message):
         parser.add_argument("--use-cache", action=argparse.BooleanOptionalAction)
         parser.add_argument("--create-local-c-file", action=argparse.BooleanOptionalAction)
         parser.add_argument("--annotate", action=argparse.BooleanOptionalAction)
-        parser.add_argument("--view-annotate", action=argparse.BooleanOptionalAction)
+        parser.add_argument("--view-annotate", choices=["none", "auto", "webbrowser", "displayhtml"],
+                            nargs="?", const="auto", default="none")
         parser.add_argument("--sage-namespace", action=argparse.BooleanOptionalAction)
         parser.add_argument("--create-local-so-file", action=argparse.BooleanOptionalAction)
         args = parser.parse_args(shlex.split(line))
-        return cython_compile(cell, **{k: v for k, v in args.__dict__.items() if v is not None})
+        view_annotate = args.view_annotate
+        del args.view_annotate
+        if view_annotate == "auto":
+            if _running_in_notebook():
+                view_annotate = "displayhtml"
+            else:
+                view_annotate = "webbrowser"
+        args_dict = {k: v for k, v in args.__dict__.items() if v is not None}
+        if view_annotate != "none":
+            args_dict["view_annotate"] = True
+            if view_annotate == "displayhtml":
+                path_to_annotate_html_container = []
+                cython_compile(cell, **args_dict, view_annotate_callback=path_to_annotate_html_container.append)
+                return HTML(filename=path_to_annotate_html_container[0])
+        return cython_compile(cell, **args_dict)
 
     @cell_magic
     def fortran(self, line, cell):

From 011fd6caa4864a88b0f49817bb0a99fc7e80b755 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Sat, 7 Dec 2024 23:29:18 +0700
Subject: [PATCH 05/11] Fix pyright

---
 src/sage/repl/ipython_extension.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 34d7d15c36f..9e1645e22df 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -66,7 +66,7 @@
 
 from IPython.core.magic import Magics, magics_class, line_magic, cell_magic
 from IPython.core.display import HTML
-from IPython import get_ipython
+from IPython.core.getipython import get_ipython
 
 from sage.repl.load import load_wrap
 from sage.env import SAGE_IMPORTALL, SAGE_STARTUP_FILE

From 0fc93c2951025b7161d001b81fb338a9660cbd9b Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Thu, 12 Dec 2024 21:14:11 +0700
Subject: [PATCH 06/11] Add a test for view-annotate=displayhtml

---
 src/sage/repl/ipython_extension.py | 36 ++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 9e1645e22df..c159f193ec5 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -358,6 +358,12 @@ def cython(self, line, cell):
         This is syntactic sugar on the
         :func:`~sage.misc.cython.cython_compile` function.
 
+        Note that there is also the ``%%cython`` cell magic provided by Cython,
+        which can be loaded with ``%load_ext cython``, see
+        `Cython documentation <https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#compiling-with-a-jupyter-notebook>`_
+        for more details.
+        The semantic is slightly different from the version provided by Sage.
+
         INPUT:
 
         - ``line`` -- parsed as keyword arguments. The allowed arguments are:
@@ -433,6 +439,36 @@ def cython(self, line, cell):
             ....: ''')
             UsageError: argument --view-annotate: invalid choice: 'xx' (choose from 'none', 'auto', 'webbrowser', 'displayhtml')
 
+        Test ``--view-annotate=displayhtml`` (note that in a notebook environment
+        an inline HTML frame will be displayed)::
+
+            sage: # needs sage.misc.cython
+            sage: shell.run_cell('''
+            ....: %%cython --view-annotate=displayhtml
+            ....: print(1)
+            ....: ''')
+            1
+            <IPython.core.display.HTML object>
+
+        Test ``--view-annotate=webbrowser``::
+
+            sage: # needs sage.misc.cython webbrowser
+            sage: shell.run_cell('''
+            ....: %%cython --view-annotate
+            ....: print(1)
+            ....: ''')
+            1
+            sage: shell.run_cell('''
+            ....: %%cython --view-annotate=auto
+            ....: print(1)
+            ....: ''')
+            1
+            sage: shell.run_cell('''
+            ....: %%cython --view-annotate=webbrowser
+            ....: print(1)
+            ....: ''')
+            1
+
         Test invalid quotes::
 
             sage: # needs sage.misc.cython

From 1551def6d18f82cd8cc91c6b8afe69b7a15c87c1 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Sun, 22 Dec 2024 20:29:34 +0700
Subject: [PATCH 07/11] Retrigger CI


From 0069cf13bd260864fce7c2d15363e4f390930f69 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Mon, 23 Dec 2024 12:48:35 +0700
Subject: [PATCH 08/11] Apply suggested changes

---
 src/sage/misc/cython.py            | 6 +++---
 src/sage/repl/ipython_extension.py | 9 ++++-----
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index f77b5afcdd5..fde36372712 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -117,7 +117,7 @@ def cython(filename, verbose=0, compile_message=False,
     - ``view_annotate_callback`` -- function (default: ``webbrowser.open``); a function
       that takes a string being the path to the html file. This can be overridden to
       change what to do with the annotated html file. Have no effect unless
-      ``view_annotate`` is ``True``
+      ``view_annotate`` is ``True``.
 
     - ``sage_namespace`` -- boolean (default: ``True``); if ``True``, import
       ``sage.all``
@@ -250,7 +250,7 @@ def cython(filename, verbose=0, compile_message=False,
         ....: ''', view_annotate=True, annotate=False)
         Traceback (most recent call last):
         ...
-        ValueError: Cannot view annotated file without creating it
+        ValueError: cannot view annotated file without creating it
 
     ::
 
@@ -420,7 +420,7 @@ def cython(filename, verbose=0, compile_message=False,
 
     if view_annotate:
         if not annotate:
-            raise ValueError("Cannot view annotated file without creating it")
+            raise ValueError("cannot view annotated file without creating it")
         view_annotate_callback(os.path.join(target_dir, name + ".html"))
 
     # This emulates running "setup.py build" with the correct options
diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index c159f193ec5..4f75c563253 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -382,13 +382,12 @@ def cython(self, line, cell):
 
           For ``--view-annotate``, the following additional choices are allowed:
 
-          - ``--view-annotate=none`` (default)
-          - ``--view-annotate=auto`` (same as ``--view-annotate``); select one of the
-            choices below automatically
+          - ``--view-annotate=none`` (default); do not view the annotated html file
+          - ``--view-annotate`` (alternatively ``--view-annotate=auto``); select one of the
+            choices below automatically: use ``webbrowser`` in the Sage command line
+            and ``displayhtml`` in the Sage notebook
           - ``--view-annotate=webbrowser``; open the annotation in a web browser
-            (preferred if the Sage command line is used)
           - ``--view-annotate=displayhtml``; display the annotation inline in the notebook
-            (preferred if the Sage notebook is used)
 
         - ``cell`` -- string; the Cython source code to process
 

From eb50b657af40a9d11b044a16d7ea7f0747033d98 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Mon, 23 Dec 2024 16:42:09 +0700
Subject: [PATCH 09/11] Simplify documentation of --view-annotate

---
 src/sage/repl/ipython_extension.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 4f75c563253..6c28c03f3da 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -380,14 +380,12 @@ def cython(self, line, cell):
 
           See :func:`~sage.misc.cython.cython` for details.
 
-          For ``--view-annotate``, the following additional choices are allowed:
+          If ``--view-annotate`` is given, the annotation is either displayed
+          inline in the Sage notebook or opened in a new web browser, depends
+          on whether the Sage notebook is used.
 
-          - ``--view-annotate=none`` (default); do not view the annotated html file
-          - ``--view-annotate`` (alternatively ``--view-annotate=auto``); select one of the
-            choices below automatically: use ``webbrowser`` in the Sage command line
-            and ``displayhtml`` in the Sage notebook
-          - ``--view-annotate=webbrowser``; open the annotation in a web browser
-          - ``--view-annotate=displayhtml``; display the annotation inline in the notebook
+          You can override the selection by specifying
+          ``--view-annotate=webbrowser`` or ``--view-annotate=displayhtml``.
 
         - ``cell`` -- string; the Cython source code to process
 
@@ -460,7 +458,7 @@ def cython(self, line, cell):
             sage: shell.run_cell('''
             ....: %%cython --view-annotate=auto
             ....: print(1)
-            ....: ''')
+            ....: ''')  # --view-annotate=auto is undocumented feature, equivalent to --view-annotate
             1
             sage: shell.run_cell('''
             ....: %%cython --view-annotate=webbrowser

From d3e23a70403a598a0421a4549bde02ac8d975d65 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:45:45 +0700
Subject: [PATCH 10/11] Apply suggested changes

---
 src/sage/repl/ipython_extension.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sage/repl/ipython_extension.py b/src/sage/repl/ipython_extension.py
index 6c28c03f3da..0818b0033b2 100644
--- a/src/sage/repl/ipython_extension.py
+++ b/src/sage/repl/ipython_extension.py
@@ -381,7 +381,7 @@ def cython(self, line, cell):
           See :func:`~sage.misc.cython.cython` for details.
 
           If ``--view-annotate`` is given, the annotation is either displayed
-          inline in the Sage notebook or opened in a new web browser, depends
+          inline in the Sage notebook or opened in a new web browser, depending
           on whether the Sage notebook is used.
 
           You can override the selection by specifying

From 61166967838d8e8aba0baf3f22d5dcea28775936 Mon Sep 17 00:00:00 2001
From: user202729 <25191436+user202729@users.noreply.github.com>
Date: Mon, 23 Dec 2024 20:33:05 +0700
Subject: [PATCH 11/11] Convert file path to URI before pass to
 webbrowser.open()

---
 src/sage/misc/cython.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
index fde36372712..29c013eab19 100644
--- a/src/sage/misc/cython.py
+++ b/src/sage/misc/cython.py
@@ -25,6 +25,7 @@
 import sys
 import shutil
 import webbrowser
+from pathlib import Path
 
 from sage.env import (SAGE_LOCAL, cython_aliases,
                       sage_include_directories)
@@ -79,9 +80,16 @@ def _standard_libs_libdirs_incdirs_aliases():
 sequence_number = {}
 
 
+def _webbrowser_open_file(path):
+    """
+    Open a html file in a web browser.
+    """
+    webbrowser.open(Path(path).as_uri())
+
+
 def cython(filename, verbose=0, compile_message=False,
            use_cache=False, create_local_c_file=False, annotate=True, view_annotate=False,
-           view_annotate_callback=webbrowser.open, sage_namespace=True, create_local_so_file=False):
+           view_annotate_callback=_webbrowser_open_file, sage_namespace=True, create_local_so_file=False):
     r"""
     Compile a Cython file. This converts a Cython file to a C (or C++ file),
     and then compiles that. The .c file and the .so file are
@@ -112,11 +120,11 @@ def cython(filename, verbose=0, compile_message=False,
       then save a copy of the .html file in the current directory.
 
     - ``view_annotate`` -- boolean (default: ``False``); if ``True``, open the
-      annotated html file in a web browser using :func:`webbrowser.open`
+      annotated html file in a web browser
 
-    - ``view_annotate_callback`` -- function (default: ``webbrowser.open``); a function
-      that takes a string being the path to the html file. This can be overridden to
-      change what to do with the annotated html file. Have no effect unless
+    - ``view_annotate_callback`` -- function; a function that takes a string
+      being the path to the html file. This can be overridden to change
+      what to do with the annotated html file. Have no effect unless
       ``view_annotate`` is ``True``.
 
     - ``sage_namespace`` -- boolean (default: ``True``); if ``True``, import