[bug#71884] [PATCH 0/3] python-dolfin-adjoint: Refresh package style.

[bug#71884] [PATCH 0/3] python-dolfin-adjoint: Refresh package style.

[Sharlatan Hellseher]

Hi Guix!

While checking CI <http://ci.guix.gnu.org/build/5043616/log/raw>, I noticed
that the package would need to be refreshed. I mistakenly thought it was
failing to build, but it actually failed to complete the build due to a
timeout with other dependencies, specifically fenics-dolfin.

Sharlatan Hellseher (3):
  gnu: python-dolfin-adjoint: Fix indentation.
  gnu: python-dolfin-adjoint: Adjust package style.
  gnu: python-dolfin-adjoint: Swap to pyproject-build-system.

 gnu/packages/simulation.scm | 122 +++++++++++++++++-------------------
 1 file changed, 58 insertions(+), 64 deletions(-)


base-commit: 85012e64819b39fd6112038134548b415fd5daff
-- 
2.41.0

[bug#71884] [PATCH 1/3] gnu: python-dolfin-adjoint: Fix indentation.

[Sharlatan Hellseher]

* gnu/packages/simulation.scm (python-dolfin-adjoint): Fix indentation.

Change-Id: I457639a98f1ae49d43042e557352d390afc9419d
---
 gnu/packages/simulation.scm | 48 ++++++++++++++++++-------------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 4fa2e93d81..ab86e1d792 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1180,29 +1180,29 @@ (define-public python-dolfin-adjoint
     (name "python-dolfin-adjoint")
     (version "2019.1.0")
     (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://github.com/dolfin-adjoint/pyadjoint")
-              (commit version)))
-        (file-name (git-file-name name version))
-        (sha256
-          (base32
-           "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
-        (modules '((guix build utils)))
-        (snippet
-         '(begin
-            ;; One of the migration tests attempts to call openmpi
-            ;; recursively and fails.  See
-            ;; https://bitbucket.org/mpi4py/mpi4py/issues/95.  Run the
-            ;; test sequentially instead.
-            (with-directory-excursion "tests/migration/optimal_control_mms"
-              (substitute* "test_optimal_control_mms.py"
-                (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
-            ;; Result files are regenerated in the check phase.
-            (delete-file-recursively
-             "tests/migration/viscoelasticity/test-results")
-            #t))))
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dolfin-adjoint/pyadjoint")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; One of the migration tests attempts to call openmpi
+           ;; recursively and fails.  See
+           ;; https://bitbucket.org/mpi4py/mpi4py/issues/95.  Run the
+           ;; test sequentially instead.
+           (with-directory-excursion "tests/migration/optimal_control_mms"
+             (substitute* "test_optimal_control_mms.py"
+               (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
+           ;; Result files are regenerated in the check phase.
+           (delete-file-recursively
+            "tests/migration/viscoelasticity/test-results")
+           #t))))
     (build-system python-build-system)
     (inputs
      (list fenics openmpi pybind11))
@@ -1219,7 +1219,7 @@ (define-public python-dolfin-adjoint
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'build 'mpi-setup
-                    ,%openmpi-setup)
+           ,%openmpi-setup)
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((doc (string-append (assoc-ref outputs "out")
-- 
2.41.0

[bug#71884] [PATCH 2/3] gnu: python-dolfin-adjoint: Adjust package style.

[Sharlatan Hellseher]

* gnu/packages/simulation.scm (python-dolfin-adjoint): Move inputs after
arguments.
[description]: Place it on a new line, fix indentation.

Change-Id: I3d971e48b4072258ed0b41af5c202e64af9de8f3
---
 gnu/packages/simulation.scm | 40 ++++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index ab86e1d792..5341c0ae55 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1204,17 +1204,6 @@ (define-public python-dolfin-adjoint
             "tests/migration/viscoelasticity/test-results")
            #t))))
     (build-system python-build-system)
-    (inputs
-     (list fenics openmpi pybind11))
-    (native-inputs
-     (list pkg-config
-           python-coverage
-           python-decorator
-           python-flake8
-           python-pkgconfig
-           python-pytest))
-    (propagated-inputs
-     `(("scipy" ,python-scipy)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -1245,17 +1234,28 @@ (define-public python-dolfin-adjoint
          ;; fails with an ImportError if it sees that the backend module
          ;; has already been loaded.
          (delete 'sanity-check))))
+    (inputs
+     (list fenics openmpi pybind11))
+    (native-inputs
+     (list pkg-config
+           python-coverage
+           python-decorator
+           python-flake8
+           python-pkgconfig
+           python-pytest))
+    (propagated-inputs
+     (list python-scipy))
     (home-page "https://www.dolfin-adjoint.org")
     (synopsis "Automatic differentiation library")
-    (description "@code{python-dolfin-adjoint} is a solver of
-differential equations associated with a governing system and a
-functional of interest.  Working from the forward model the solver
-automatically derives the discrete adjoint and tangent linear models.
-These additional models are key ingredients in many algorithms such as
-data assimilation, optimal control, sensitivity analysis, design
-optimisation and error estimation.  The dolfin-adjoint project
-provides the necessary tools and data structures for cases where the
-forward model is implemented in @code{fenics} or
+    (description
+     "@code{python-dolfin-adjoint} is a solver of differential equations
+associated with a governing system and a functional of interest.  Working from
+the forward model the solver automatically derives the discrete adjoint and
+tangent linear models.  These additional models are key ingredients in many
+algorithms such as data assimilation, optimal control, sensitivity analysis,
+design optimisation and error estimation.  The dolfin-adjoint project provides
+the necessary tools and data structures for cases where the forward model is
+implemented in @code{fenics} or
 @url{https://firedrakeproject.org,firedrake}.")
     (license license:lgpl3)))
 
-- 
2.41.0

[bug#71884] [PATCH 3/3] gnu: python-dolfin-adjoint: Swap to pyproject-build-system.

[Sharlatan Hellseher]

* gnu/packages/simulation.scm (python-dolfin-adjoint) [source]: Remove
trailing #t from snippet.
[build-system]: Swap to pyproject-build-system.
[arguments]: Apply G-expressions. <#:phases>: Swap back to defaul 'check
phase.

python-dolfin-adjoint

Change-Id: Idf100b718b44d9d6695e598c434fbbac55a38845
---
 gnu/packages/simulation.scm | 58 +++++++++++++++++--------------------
 1 file changed, 26 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 5341c0ae55..182e00cec4 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1201,39 +1201,33 @@ (define-public python-dolfin-adjoint
                (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
            ;; Result files are regenerated in the check phase.
            (delete-file-recursively
-            "tests/migration/viscoelasticity/test-results")
-           #t))))
-    (build-system python-build-system)
+            "tests/migration/viscoelasticity/test-results")))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'build 'mpi-setup
-           ,%openmpi-setup)
-         (add-after 'install 'install-doc
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((doc (string-append (assoc-ref outputs "out")
-                                        "/share/doc/" ,name "-"
-                                        ,version))
-                    (examples (string-append doc "/examples")))
-               (mkdir-p examples)
-               (copy-recursively "examples" examples))
-             #t))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (setenv "HOME" (getcwd))
-               (and (invoke "py.test" "-v" "tests/fenics_adjoint"
-                            "-k" "not test_read_checkpoint")
-                    (invoke "py.test" "-v" "tests/migration")
-                    (invoke "py.test" "-v" "tests/pyadjoint")))
-             #t))
-         ;; Remove 'sanity-check, because it tries to import
-         ;; firedrake_adjoint after importing fenics_adjoint.
-         ;; Both load a module named 'backend' and firedrake_adjoint
-         ;; fails with an ImportError if it sees that the backend module
-         ;; has already been loaded.
-         (delete 'sanity-check))))
+     (list
+      #:test-flags
+      #~(list "tests/firedrake_adjoint/"
+              "tests/migration"
+              "tests/pyadjoint/"
+              "-k" "not test_read_checkpoint")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'build 'mpi-setup ,%openmpi-setup)
+          (add-before 'check 'set-environment-variables
+            (lambda _
+              (setenv "HOME" "/tmp")))
+          (add-after 'install 'install-doc
+            (lambda _
+              (let* ((doc (string-append #$output "/share/doc/" name "-" version))
+                     (examples (string-append doc "/examples")))
+                (mkdir-p examples)
+                (copy-recursively "examples" examples))))
+          ;; Remove 'sanity-check, because it tries to import
+          ;; firedrake_adjoint after importing fenics_adjoint.
+          ;; Both load a module named 'backend' and firedrake_adjoint
+          ;; fails with an ImportError if it sees that the backend module
+          ;; has already been loaded.
+          (delete 'sanity-check))))
     (inputs
      (list fenics openmpi pybind11))
     (native-inputs
-- 
2.41.0