[bug#62622] [PATCH 0/8] Update proj and a few other geo packages

[bug#62622] [PATCH 0/8] Update proj and a few other geo packages

[Felix Gruber]

This patchset updates a few geographical packages and makes sure that
their dependents still build. I've also updated the qgis package and
overhauled its 'check target to run tests in parallel and define an
environment variable (which was already defined in the wrapper script
that gets installed) that is needed by a few tests to succeed.

Felix Gruber (8):
  gnu: geos: Update to 3.11.2.
  gnu: proj: Update to 9.2.0.
  gnu: python-pyproj: Update to 3.5.0.
  gnu: python-cartopy: Update to 0.21.1.
  gnu: python-rtree: Update to 1.0.1.
  gnu: python-osmnx: Use pyproject-build-system.
  gnu: pcb2gcode: Update to 2.5.0.
  gnu: qgis: Update to 3.30.1.

 gnu/packages/engineering.scm |  61 ++++++------
 gnu/packages/geo.scm         | 173 +++++++++++++++++++----------------
 2 files changed, 121 insertions(+), 113 deletions(-)

-- 
2.39.2

[bug#62622] [PATCH 1/8] gnu: geos: Update to 3.11.2.

[Felix Gruber]

* gnu/packages/geo.scm (geos): Update to 3.11.2.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 753ab558ad..95ead23e10 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -291,7 +291,7 @@ (define-public memphis
 (define-public geos
   (package
     (name "geos")
-    (version "3.11.1")
+    (version "3.11.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.osgeo.org/geos/geos-"
@@ -299,7 +299,7 @@ (define-public geos
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1qhbirv1rbznv99ha0pa0zybvcsn0dsz2xfc65vr8bgrm77v63kd"))))
+                "1k744nwfa5sj4amzsdjxgac83wh6xfb9xi7z5bka7ic1jik7gw5i"))))
     (build-system cmake-build-system)
     (arguments `(#:phases
                  (modify-phases %standard-phases
-- 
2.39.2

[bug#62622] [PATCH 2/8] gnu: proj: Update to 9.2.0.

[Felix Gruber]

* gnu/packages/geo.scm (proj): Update to 9.2.0.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 95ead23e10..47ef8b8a89 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -598,7 +598,7 @@ (define-public libspatialite
 (define-public proj
   (package
     (name "proj")
-    (version "9.1.1")
+    (version "9.2.0")
     (source
      (origin
        (method url-fetch)
@@ -606,7 +606,7 @@ (define-public proj
                            version ".tar.gz"))
        (sha256
         (base32
-         "0fbd1vj4cj19kwh03vdn0a4hr0xaacvi876yyyw5xfsj1q0x8g00"))))
+         "03nm1sgvh237my7ss6kayn6887cbnayvjxrrxsrfcakkmbsida6y"))))
     (build-system cmake-build-system)
     (native-inputs (list googletest pkg-config))
     (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
-- 
2.39.2

[bug#62622] [PATCH 3/8] gnu: python-pyproj: Update to 3.5.0.

[Felix Gruber]

* gnu/packages/geo.scm (python-pyproj): Update to 3.5.0.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 47ef8b8a89..8c93f86dd2 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -700,14 +700,14 @@ (define-public proj.4
 (define-public python-pyproj
   (package
     (name "python-pyproj")
-    (version "3.4.0")
+    (version "3.5.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyproj" version))
         (sha256
           (base32
-            "0czbfl5dd7jckbwvinfwiwdb99sxj796gfn3a9zqbsdc4xcl8257"))))
+            "1xhvr0n5gb7v6x0wd7cqmc0zrky2fag7bq2shx6l2qqq3icx2ncq"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.39.2

[bug#62622] [PATCH 4/8] gnu: python-cartopy: Update to 0.21.1.

[Felix Gruber]

* gnu/packages/geo.scm (python-cartopy): Update to 0.21.1.
---
 gnu/packages/geo.scm | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 8c93f86dd2..344ffae8fb 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1183,8 +1183,17 @@ (define-public python-cartopy
                (invoke "python" "-m" "pytest" "--pyargs" "cartopy"
                        ;; These tests require online data.
                        "-m" "not natural_earth and not network"
-                       ;; This one too but it's not marked as such.
-                       "-k" "not test_gridliner_labels_bbox_style")))))))
+                       "-k"
+                       (string-append
+                         ;; This one too but it's not marked as such.
+                         "not test_gridliner_labels_bbox_style"
+                         ;; Those tests fail with proj 9.2.0
+                         ;; https://github.com/SciTools/cartopy/issues/2145
+                         " and not test_epsg"
+                         " and not test_default"
+                         " and not test_eccentric_globe"
+                         " and not test_ellipsoid_transform"
+                         " and not test_eccentric_globe"))))))))
     (propagated-inputs
      (list python-matplotlib
            python-numpy
-- 
2.39.2

[bug#62622] [PATCH 5/8] gnu: python-rtree: Update to 1.0.1.

[Felix Gruber]

* gnu/packages/geo.scm (python-rtree): Update to 1.0.1.
  [build-system]: Use pyproject-build-system instead of
  python-build-system.
  [arguments]: Remove custom 'check phase.
---
 gnu/packages/geo.scm | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 344ffae8fb..e046797a3f 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1655,14 +1655,14 @@ (define-public libspatialindex
 (define-public python-rtree
   (package
     (name "python-rtree")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Rtree" version))
        (sha256
-        (base32 "10lnhf67c9pb0yisxdqmb52dy6lj1za1h9d4p69v0ihk2a138j6h"))))
-    (build-system python-build-system)
+        (base32 "0aalh07fyf6vpr0a6zswnqvvrjhyic1zg6w4bl368fihkilj2892"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -1672,11 +1672,7 @@ (define-public python-rtree
                (substitute* "rtree/finder.py"
                  (("find_library\\(\"spatialindex_c\"\\)")
                   (string-append  "\"" libspatialindex
-                                  "/lib/libspatialindex_c.so\""))))))
-         (replace 'check
-           (lambda* (#:key outputs tests? #:allow-other-keys)
-             (when tests?
-                 (invoke "pytest")))))))
+                                  "/lib/libspatialindex_c.so\"")))))))))
     (native-inputs
      (list python-numpy python-pytest python-wheel))
     (inputs
-- 
2.39.2

[bug#62622] [PATCH 6/8] gnu: python-osmnx: Use pyproject-build-system.

[Felix Gruber]

* gnu/packages/geo.scm (python-osmnx)[build-system]: Use
  pyproject-build-system instead of python-build-system.
  [arguments]: Remove custom 'check phase. Instead define test-flags to
  disable network tests.
---
 gnu/packages/geo.scm | 41 ++++++++++++++++++-----------------------
 1 file changed, 18 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index e046797a3f..76a42c4140 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -44,6 +44,7 @@ (define-module (gnu packages geo)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix gexp)
@@ -854,30 +855,24 @@ (define-public python-osmnx
        (file-name (git-file-name name version))
        (sha256
         (base32 "1n8qjn184p5a2s3j6x6iyc1i7p3l3xnbqqxm6ajwgwv6j5fw1d5a"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               ; TODO: Disable network tests
-               (invoke "pytest" "tests"
-                       "-k"
-                       (string-append
-                         ;; The following tests require network access.
-                         "not test_geocode_to_gdf"
-                         " and not test_stats"
-                         " and not test_osm_xml"
-                         " and not test_elevation"
-                         " and not test_routing"
-                         " and not test_plots"
-                         " and not test_find_nearest"
-                         " and not test_api_endpoints"
-                         " and not test_graph_save_load"
-                         " and not test_graph_from_functions"
-                         " and not test_geometries"))))))))
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; The following tests require network access.
+               "not test_geocode_to_gdf"
+               " and not test_stats"
+               " and not test_osm_xml"
+               " and not test_elevation"
+               " and not test_routing"
+               " and not test_plots"
+               " and not test_find_nearest"
+               " and not test_api_endpoints"
+               " and not test_graph_save_load"
+               " and not test_graph_from_functions"
+               " and not test_geometries"))))
     (propagated-inputs
       (list python-folium
             python-geopandas
-- 
2.39.2

[bug#62622] [PATCH 7/8] gnu: pcb2gcode: Update to 2.5.0.

[Felix Gruber]

* gnu/packages/engineering.scm (pcb2gcode): Update to 2.5.0.
---
 gnu/packages/engineering.scm | 61 +++++++++++++++++-------------------
 1 file changed, 29 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 18f2d024b1..6bd4cadfc3 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -35,7 +35,7 @@
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
-;;; Copyright © 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2022, 2023 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3083,40 +3083,37 @@ (define-public emacs-poke
 @code{Poke Ras mode} and @code{Poke Map mode}.")))
 
 (define-public pcb2gcode
-  ;; Take some additional commits after v2.4.0 to fix build against
-  ;; geos 3.10.1.
-  (let ((commit "ae41f9fe41e57ee5d0cced6c3b3c8aea9c3f5392"))
-    (package
-     (name "pcb2gcode")
-     (version (git-version "2.4.0" "1" commit))
-     (source
-      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/pcb2gcode/pcb2gcode")
-             (commit commit)
-             (recursive? #t)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "1r1qmvpn5ffi2xpq2gigwsk8kn79s4s2ywfvicwf8i7rzwhkdf17"))))
-     (build-system gnu-build-system)
-     (inputs
-      (list boost
-            geos
-            gerbv
-            glibmm
-            gtkmm-2
-            librsvg))
-     (native-inputs
-      (list autoconf automake libtool pkg-config))
-     (home-page "https://github.com/pcb2gcode/pcb2gcode")
-     (synopsis "Generate G-code for milling PCBs")
-     (description "pcb2gcode is a command-line program for isolation routing
+  (package
+   (name "pcb2gcode")
+   (version "2.5.0")
+   (source
+    (origin
+     (method git-fetch)
+     (uri (git-reference
+           (url "https://github.com/pcb2gcode/pcb2gcode")
+           (commit (string-append "v" version))
+           (recursive? #t)))
+     (file-name (git-file-name name version))
+     (sha256
+      (base32
+       "01s41znkcq9x1rinsdqrrdj8p35isckrcxs14ajsi7wr39n1m5kk"))))
+   (build-system gnu-build-system)
+   (inputs
+    (list boost
+          geos
+          gerbv
+          glibmm
+          gtkmm-2
+          librsvg))
+   (native-inputs
+    (list autoconf automake libtool pkg-config))
+   (home-page "https://github.com/pcb2gcode/pcb2gcode")
+   (synopsis "Generate G-code for milling PCBs")
+   (description "pcb2gcode is a command-line program for isolation routing
 and drilling of PCBs.  It takes Gerber files as input and outputs G-code files
 for the milling of PCBs.  It also includes an autoleveller for the automatic
 dynamic calibration of the milling depth.")
-     (license license:gpl3+))))
+   (license license:gpl3+)))
 
 ;; libdxfrw has no readme, no version release, no tags.  Initial commit says
 ;; "libdxfrw-0.6.3 import", but it shares no git history with "upstream"
-- 
2.39.2

[bug#62622] [PATCH 8/8] gnu: qgis: Update to 3.30.1.

[Felix Gruber]

* gnu/packages/geo.scm (qgis): Update to 3.30.1.
  [arguments]: Define GISBASE environment variable during tests as it
  is used to find Grass GIS. (later in the installed version of QGis the
  same environment variable has already been set.)
  Execute tests in parallel.
  Update list of disabled broken tests. Try to classify failure reasons
  (network, missing/incomplete dependencies). There are still a lot of
  tests with unknown failure reasons.
---
 gnu/packages/geo.scm | 95 ++++++++++++++++++++++++--------------------
 1 file changed, 53 insertions(+), 42 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 76a42c4140..77f6f853b4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -13,7 +13,7 @@
 ;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
-;;; Copyright © 2020, 2021, 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
@@ -2464,14 +2464,14 @@ (define-public saga
 (define-public qgis
   (package
     (name "qgis")
-    (version "3.26.2")
+    (version "3.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://qgis.org/downloads/qgis-"
                            version ".tar.bz2"))
        (sha256
-        (base32 "1hsq3wchsf7db7134fgg9xzzap35q1s4r6649d0krbw80xw5asca"))))
+        (base32 "0mdgqyqr3nswp5qfpjrpr35lxizcrz73a1gs3ddxsd1xr9amzb5s"))))
     (build-system cmake-build-system)
     (arguments
      `(#:modules ((guix build cmake-build-system)
@@ -2513,20 +2513,56 @@ (define-public qgis
                (("\\$\\(git rev-parse --show-toplevel\\)")
                 (getcwd)))))
          (replace 'check
-           (lambda* (#:key inputs tests? #:allow-other-keys)
+           (lambda* (#:key inputs outputs tests? parallel-tests?
+                     #:allow-other-keys)
              (when tests?
              (setenv "HOME" "/tmp")
              (system "Xvfb :1 &")
              (setenv "DISPLAY" ":1")
              (setenv "TRAVIS" "true")
              (setenv "CTEST_OUTPUT_ON_FAILURE" "1")
+             (let* ((out (assoc-ref outputs "out"))
+                    (grass-version ,(package-version grass))
+                    (grass-majorminor (string-join
+                                       (list-head
+                                        (string-split grass-version #\.) 2)
+                                       ""))
+                    (grass (string-append (assoc-ref inputs "grass")
+                                          "/grass" grass-majorminor)))
+               (setenv "GISBASE" grass))
              (invoke "ctest"
+                     "-j" (if parallel-tests?
+                              (number->string (parallel-job-count))
+                              "1")
                      "-E" (string-join
                            '(;; Disable tests that require network access
+                             "PyQgsExternalStorageAwsS3"
+                             "PyQgsExternalStorageWebDav"
                              "qgis_filedownloader"
+                             "test_core_networkaccessmanager"
+                             "test_core_tiledownloadmanager"
+                             "test_gui_filedownloader"
+                             "test_provider_wcsprovider"
+                             ;; Disable tests that need OGR built with
+                             ;; libspatialite support
+                             "PyQgsAttributeTableModel"
+                             "PyQgsOGRProviderSqlite"
+                             "PyQgsWFSProvider"
+                             "PyQgsOapifProvider"
+                             ;; Disable tests that need Python compiled
+                             ;; with loadable SQLite extensions.
+                             "PyQgsFieldFormattersTest"
+                             "PyQgsSpatialiteProvider"
+                             "PyQgsLayerDependencies"
+                             "PyQgsDBManagerGpkg"
+                             "PyQgsDBManagerSpatialite"
+                             ;; Disable tests that need poppler (with Cairo)
+                             "PyQgsLayoutExporter"
+                             "PyQgsPalLabelingLayout"
+                             ;; Disable tests that need Orfeo ToolBox
+                             "ProcessingOtbAlgorithmsTest"
                              ;; TODO: Find why the following tests fail
                              "ProcessingQgisAlgorithmsTestPt1"
-                             "ProcessingQgisAlgorithmsTestPt2"
                              "ProcessingQgisAlgorithmsTestPt3"
                              "ProcessingQgisAlgorithmsTestPt4"
                              "ProcessingGdalAlgorithmsRasterTest"
@@ -2535,68 +2571,42 @@ (define-public qgis
                              "ProcessingGrass7AlgorithmsRasterTestPt1"
                              "ProcessingGrass7AlgorithmsRasterTestPt2"
                              "ProcessingGrass7AlgorithmsVectorTest"
-                             "ProcessingOtbAlgorithmsTest"
                              "test_core_authmanager"
                              "test_core_compositionconverter"
-                             "test_core_coordinatereferencesystem"
+                             "test_core_expression"
                              "test_core_gdalutils"
-                             "test_core_labelingengine"
-                             "test_core_layout"
-                             "test_core_layouthtml"
-                             "test_core_layoutlabel"
-                             "test_core_layoutmultiframe"
                              "test_core_layoutpicture"
-                             "test_core_legendrenderer"
-                             "test_core_networkaccessmanager"
-                             "test_core_rasterfilewriter"
-                             "test_core_tiledownloadmanager"
-                             "test_gui_dualview"
-                             "test_gui_htmlwidgetwrapper"
-                             "test_gui_filedownloader"
+                             "test_core_pointcloudlayerexporter"
+                             "test_core_projectstorage"
+                             "test_core_coordinatereferencesystem"
                              "test_gui_queryresultwidget"
+                             "test_provider_copcprovider"
+                             "test_analysis_processingalgspt1"
                              "test_analysis_processingalgspt2"
                              "test_analysis_processing"
-                             "test_provider_wcsprovider"
-                             "qgis_grassprovidertest7"
-                             "test_app_gpsinformationwidget"
+                             "test_app_gpsintegration"
                              "PyQgsAnnotation"
-                             "PyQgsAttributeTableModel"
                              "PyQgsAuthenticationSystem"
-                             "PyQgsExternalStorageWebDAV"
-                             "PyQgsFieldFormattersTest"
+                             "PyQgsDatumTransform"
                              "PyQgsFileUtils"
                              "PyQgsGeometryTest"
                              "PyQgsGoogleMapsGeocoder"
+                             "PyQgsGroupLayer"
                              "PyQgsHashLineSymbolLayer"
-                             "PyQgsLayoutExporter"
                              "PyQgsLayoutHtml"
                              "PyQgsLineSymbolLayers"
                              "PyQgsMapLayer"
-                             "PyQgsNetworkContentFetcherRegistry"
                              "PyQgsOGRProviderGpkg"
-                             "PyQgsOGRProviderSqlite"
-                             "PyQgsPalLabelingCanvas"
-                             "PyQgsPalLabelingLayout"
-                             "PyQgsPalLabelingPlacement"
-                             "PyQgsProcessExecutable"
+                             "PyQgsProcessExecutablePt1"
+                             "PyQgsProcessExecutablePt2"
                              "PyQgsProviderConnectionGpkg"
                              "PyQgsProviderConnectionSpatialite"
                              "PyQgsOGRProvider"
-                             "PyQgsSpatialiteProvider"
                              "PyQgsVectorFileWriter"
                              "PyQgsVectorLayerEditBuffer"
-                             "PyQgsVectorLayerEditBufferGroup"
-                             "PyQgsVectorLayerProfileGenerator"
                              "PyQgsVirtualLayerProvider"
-                             "PyQgsWFSProvider"
-                             "PyQgsWFSProviderGUI"
-                             "PyQgsOapifProvider"
-                             "PyQgsLayerDependencies"
-                             "PyQgsDBManagerGpkg"
-                             "PyQgsDBManagerSpatialite"
                              "PyQgsAuxiliaryStorage"
                              "PyQgsSelectiveMasking"
-                             "qgis_shellcheck"
                              "qgis_sipify"
                              "qgis_sip_include"
                              "qgis_sip_uptodate")
@@ -2665,6 +2675,7 @@ (define-public qgis
            qtdeclarative-5
            qtkeychain
            qtlocation
+           qtmultimedia-5
            qtserialport
            qtsvg-5
            qwt
-- 
2.39.2

bug#62622: [PATCH 0/8] Update proj and a few other geo packages

[Guillaume Le Vaillant]

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Patches pushed as dd1aebe148de77c098f2b430f6b7ef99d4416000 and
following, with a fixed commit message for patch 4.
Thanks.

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