gnu: Add python-pyan3.

* gnu/packages/python-xyz.scm (python-pyan3): New variable.
* gnu/packages/patches/python-pyan3-fix-absolute-path-bug.patch,
gnu/packages/patches/python-pyan3-fix-positional-arguments.patch: New files.
* gnu/local.mk: Register them.

3 files changed, 224 insertions, 0 deletions

diff --git a/gnu/packages/patches/python-pyan3-fix-absolute-path-bug.patch b/gnu/packages/patches/python-pyan3-fix-absolute-path-bug.patch
new file mode 100644
index 0000000000..0b6a083fa3
--- /dev/null
+++ b/gnu/packages/patches/python-pyan3-fix-absolute-path-bug.patch
@@ -0,0 +1,160 @@
+From ac1bd55d07fd1bad2f4a92dc0809607c407d9140 Mon Sep 17 00:00:00 2001
+From: "Maciej A. Czyzewski" <maciejanthonyczyzewski@gmail.com>
+Date: Wed, 9 Jun 2021 15:29:18 +0200
+Subject: [PATCH] feature: new params for graphviz + solves #70
+
+- solve abs path bug #70
+- new params for graphviz (ranksep; layout)
+- tested layout `dot`; `fdp` (square graph)
+- updated `.gitignore` (files gen. after `visualize_pyan_architecture.sh`)
+---
+ .gitignore                     |  5 ++++
+ README.md                      |  6 ++--
+ pyan/main.py                   | 55 +++++++++++++++++++++++++++++++---
+ visualize_pyan_architecture.sh |  5 ++++
+ 4 files changed, 64 insertions(+), 7 deletions(-)
+
+diff --git a/.gitignore b/.gitignore
+index 990fdc0c..93313aaf 100644
+--- a/.gitignore
++++ b/.gitignore
+@@ -162,3 +162,8 @@ htmlcov
+ .idea/
+ .history/
+ .vscode/
++
++# our vis. of architecture
++architecture.dot
++architecture.html
++architecture.svg
+diff --git a/README.md b/README.md
+index d1f19dcf..9e6919a3 100644
+--- a/README.md
++++ b/README.md
+@@ -48,7 +48,7 @@ See `pyan3 --help`.
+ 
+ Example:
+ 
+-`pyan *.py --uses --no-defines --colored --grouped --annotated --dot >myuses.dot`
++`pyan3 *.py --uses --no-defines --colored --grouped --annotated --dot >myuses.dot`
+ 
+ Then render using your favorite GraphViz filter, mainly `dot` or `fdp`:
+ 
+@@ -56,11 +56,11 @@ Then render using your favorite GraphViz filter, mainly `dot` or `fdp`:
+ 
+ Or use directly
+ 
+-`pyan *.py --uses --no-defines --colored --grouped --annotated --svg >myuses.svg`
++`pyan3 *.py --uses --no-defines --colored --grouped --annotated --svg >myuses.svg`
+ 
+ You can also export as an interactive HTML
+ 
+-`pyan *.py --uses --no-defines --colored --grouped --annotated --html > myuses.html`
++`pyan3 *.py --uses --no-defines --colored --grouped --annotated --html > myuses.html`
+ 
+ Alternatively, you can call `pyan` from a script
+ 
+diff --git a/pyan/main.py b/pyan/main.py
+index 5d079714..b1a16f63 100644
+--- a/pyan/main.py
++++ b/pyan/main.py
+@@ -141,6 +141,31 @@ def main(cli_args=None):
+         ),
+     )
+ 
++    parser.add_argument(
++        "--dot-ranksep",
++        default="0.5",
++        dest="ranksep",
++        help=(
++            "specifies the dot graph 'ranksep' property for "
++            "controlling desired rank separation, in inches. "
++            "Allowed values: [0.02 .. 1000.0]. "
++            "[dot only]"
++        ),
++    )
++
++    parser.add_argument(
++        "--graphviz-layout",
++        default="dot",
++        dest="layout",
++        help=(
++            "specifies the graphviz 'layout' property for "
++            "the name of the layout algorithm to use. "
++            "Allowed values: ['dot', 'neato', 'fdp', 'sfdp', 'twopi', 'circo']. "
++            "Recommended values: ['dot', 'fdp']. "
++            "[graphviz only]"
++        ),
++    )
++
+     parser.add_argument(
+         "-a",
+         "--annotated",
+@@ -159,7 +184,12 @@ def main(cli_args=None):
+ 
+     known_args, unknown_args = parser.parse_known_args(cli_args)
+ 
+-    filenames = [fn2 for fn in unknown_args for fn2 in glob(fn, recursive=True)]
++
++    filenames = []
++    for fn in unknown_args:
++        for fn2 in glob(fn, recursive=True):
++            abs_fn2 = os.path.abspath(fn2)
++            filenames.append(abs_fn2)
+ 
+     # determine root
+     if known_args.root is not None:
+@@ -203,6 +233,11 @@ def main(cli_args=None):
+         handler = logging.FileHandler(known_args.logname)
+         logger.addHandler(handler)
+ 
++    logger.debug(f"[files] {unknown_args}")
++
++    if root:
++        root = os.path.abspath(root)
++
+     v = CallGraphVisitor(filenames, logger=logger, root=root)
+ 
+     if known_args.function or known_args.namespace:
+@@ -222,13 +257,25 @@ def main(cli_args=None):
+     writer = None
+ 
+     if known_args.dot:
+-        writer = DotWriter(graph, options=["rankdir=" + known_args.rankdir], output=known_args.filename, logger=logger)
++        writer = DotWriter(graph, options=[
++            "rankdir=" + known_args.rankdir,
++            "ranksep=" + known_args.ranksep,
++            "layout=" + known_args.layout,
++        ], output=known_args.filename, logger=logger)
+ 
+     if known_args.html:
+-        writer = HTMLWriter(graph, options=["rankdir=" + known_args.rankdir], output=known_args.filename, logger=logger)
++        writer = HTMLWriter(graph, options=[
++            "rankdir=" + known_args.rankdir,
++            "ranksep=" + known_args.ranksep,
++            "layout=" + known_args.layout,
++        ], output=known_args.filename, logger=logger)
+ 
+     if known_args.svg:
+-        writer = SVGWriter(graph, options=["rankdir=" + known_args.rankdir], output=known_args.filename, logger=logger)
++        writer = SVGWriter(graph, options=[
++            "rankdir=" + known_args.rankdir,
++            "ranksep=" + known_args.ranksep,
++            "layout=" + known_args.layout,
++        ], output=known_args.filename, logger=logger)
+ 
+     if known_args.tgf:
+         writer = TgfWriter(graph, output=known_args.filename, logger=logger)
+diff --git a/visualize_pyan_architecture.sh b/visualize_pyan_architecture.sh
+index 22c63342..81b6ca24 100755
+--- a/visualize_pyan_architecture.sh
++++ b/visualize_pyan_architecture.sh
+@@ -2,3 +2,8 @@
+ echo -ne "Pyan architecture: generating architecture.{dot,svg}\n"
+ python3 -m pyan pyan/*.py --no-defines --uses --colored --annotate --dot -V >architecture.dot 2>architecture.log
+ dot -Tsvg architecture.dot >architecture.svg
++echo -ne "Pyan architecture: generating architecture.{html,graphviz=fdp}\n"
++python3 -m pyan pyan/*.py --no-defines --uses \
++	--grouped --nested-groups \
++	--graphviz-layout fdp \
++	--colored --html > architecture.html
diff --git a/gnu/packages/patches/python-pyan3-fix-positional-arguments.patch b/gnu/packages/patches/python-pyan3-fix-positional-arguments.patch
new file mode 100644
index 0000000000..81923d7a41
--- /dev/null
+++ b/gnu/packages/patches/python-pyan3-fix-positional-arguments.patch
@@ -0,0 +1,22 @@
+From 37404bb039bd9c5509b4aec8f61e360dfba50715 Mon Sep 17 00:00:00 2001
+From: Wenxin Ling <w.ling@mediaire.de>
+Date: Mon, 1 Mar 2021 15:21:16 +0100
+Subject: [PATCH] Fix positional arguments issue for CallGraphVisitor
+
+---
+ pyan/main.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/pyan/main.py b/pyan/main.py
+index 18821a14..5d079714 100644
+--- a/pyan/main.py
++++ b/pyan/main.py
+@@ -203,7 +203,7 @@ def main(cli_args=None):
+         handler = logging.FileHandler(known_args.logname)
+         logger.addHandler(handler)
+ 
+-    v = CallGraphVisitor(filenames, logger, root=root)
++    v = CallGraphVisitor(filenames, logger=logger, root=root)
+ 
+     if known_args.function or known_args.namespace:
+ 
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 56920f68c3..87a90ab680 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26232,3 +26232,45 @@ for the Go language tool chain; it adapts to different calling conventions and
 application binary interfaces (ABIs); it takes care of register allocation; it
 supports x86_64 instructions up to AVX-512 and SHA.")
       (license license:bsd-2))))
+
+(define-public python-pyan3
+  (package
+    (name "python-pyan3")
+    (version "1.2.0")
+    (source
+     (origin
+       ;; Source tarball on PyPI lacks tests.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Technologicat/pyan")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1367x25rcy2y8f0x9c2dbxl2qgdln3arr7ddyzybz2c28g6jrv5z"))
+       (patches (search-patches "python-pyan3-fix-positional-arguments.patch"
+                                "python-pyan3-fix-absolute-path-bug.patch"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               ;; Extend PYTHONPATH so the built package will be found.
+               (setenv "PYTHONPATH"
+                       (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+               (invoke "pytest")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-wheel" ,python-wheel)))
+    (propagated-inputs
+     `(("python-jinja2" ,python-jinja2)))
+    (home-page "https://github.com/Technologicat/pyan")
+    (synopsis "Offline call graph generator for Python 3")
+    (description "Pyan takes one or more Python source files, performs
+a (rather superficial) static analysis, and constructs a directed graph of the
+objects in the combined source, and how they define or use each other.  The
+graph can be output for rendering by GraphViz or yEd.")
+    (license license:gpl2)))