Bookkeeping - merge recent changes from release/4.x

Jenkinsfile

@@ -13,17 +13,18 @@
 // @Library('dragons_ci@master') _
 
 // Change these to automatically skip steps
-def runtests_unit    = 1
-def runtests_regress = 1
-def runtests_gmosls  = 1  // 1 to enable
-def runtests_slow    = 1
-def runtests_f2      = 1
-def runtests_niri    = 1
-def runtests_gsaoi   = 1
-def runtests_gnirs   = 1
-def runtests_wavecal = 1
-def runtests_ghost   = 1
-def runtests_gmos    = 1
+def runtests_unit        = 1
+def runtests_regress     = 1
+def runtests_gmosls      = 1  // 1 to enable
+def runtests_slow        = 1
+def runtests_f2          = 1
+def runtests_niri        = 1
+def runtests_gsaoi       = 1
+def runtests_gnirs       = 1
+def runtests_wavecal     = 1
+def runtests_ghost       = 1
+def runtests_gmos        = 1
+def runtests_ghost_integ = 1
 
 pipeline {
 
@@ -162,6 +163,45 @@ pipeline {
                         }
                     } // end post
                 }
+
+                stage('WaveCal Tests') {
+                    when {
+                        expression { runtests_wavecal == 1 }
+                    }
+
+                    agent { label "master" }
+                    environment {
+                        MPLBACKEND = "agg"
+                        DRAGONS_TEST_OUT = "wavecal_tests_outputs"
+                        TOX_ARGS = "astrodata geminidr gemini_instruments gempy recipe_system"
+                        TMPDIR = "${env.WORKSPACE}/.tmp/wavecal/"
+                    }
+                    steps {
+                        echo "Running build #${env.BUILD_ID} on ${env.NODE_NAME}"
+                        checkout scm
+                        sh '.jenkins/scripts/setup_dirs.sh'
+                        echo "Running tests"
+                        sh 'tox -e py312-wavecal -v -- --basetemp=${DRAGONS_TEST_OUT} --junit-xml reports/wavecal_results.xml ${TOX_ARGS}'
+                        echo "Reporting coverage"
+                        sh 'tox -e codecov -- -F wavecal'
+                    }  // end steps
+                    post {
+                        always {
+                            echo "Running 'archivePlots' from inside WaveCal Tests"
+                            archiveArtifacts artifacts: "plots/*", allowEmptyArchive: true
+                            junit (
+                                allowEmptyResults: true,
+                                testResults: '.tmp/py312-wavecal/reports/*_results.xml'
+                            )
+                            echo "Deleting WaveCal Tests workspace ${env.WORKSPACE}"
+                            cleanWs()
+                            dir("${env.WORKSPACE}@tmp") {
+                              deleteDir()
+                            }
+                        }  // end always
+                    }  // end post
+                }  // end stage
+
             } // end parallel
         }
 
@@ -355,44 +395,6 @@ pipeline {
             } // end parallel
         }
 
-        stage('WaveCal Tests') {
-            when {
-                expression { runtests_wavecal == 1 }
-            }
-
-            agent { label "master" }
-            environment {
-                MPLBACKEND = "agg"
-                DRAGONS_TEST_OUT = "wavecal_tests_outputs"
-                TOX_ARGS = "astrodata geminidr gemini_instruments gempy recipe_system"
-                TMPDIR = "${env.WORKSPACE}/.tmp/wavecal/"
-            }
-            steps {
-                echo "Running build #${env.BUILD_ID} on ${env.NODE_NAME}"
-                checkout scm
-                sh '.jenkins/scripts/setup_dirs.sh'
-                echo "Running tests"
-                sh 'tox -e py312-wavecal -v -- --basetemp=${DRAGONS_TEST_OUT} --junit-xml reports/wavecal_results.xml ${TOX_ARGS}'
-                echo "Reporting coverage"
-                sh 'tox -e codecov -- -F wavecal'
-            }  // end steps
-            post {
-                always {
-                    echo "Running 'archivePlots' from inside WaveCal Tests"
-                    archiveArtifacts artifacts: "plots/*", allowEmptyArchive: true
-                    junit (
-                        allowEmptyResults: true,
-                        testResults: '.tmp/py312-wavecal/reports/*_results.xml'
-                    )
-                    echo "Deleting WaveCal Tests workspace ${env.WORKSPACE}"
-                    cleanWs()
-                    dir("${env.WORKSPACE}@tmp") {
-                      deleteDir()
-                    }
-                }  // end always
-            }  // end post
-        }  // end stage
-
         stage('Slower tests') {
             parallel {
                 stage('GMOS LS Tests') {
@@ -507,6 +509,43 @@ pipeline {
                         }
                     } // end post
                 } // end stage
+
+                stage('GHOST Integration test') {
+                    when {
+                        expression { runtests_ghost_integ == 1 }
+                    }
+
+                    agent { label "master" }
+                    environment {
+                        MPLBACKEND = "agg"
+                        DRAGONS_TEST_OUT = "ghost_integ_tests_outputs"
+                        TOX_ARGS = "astrodata geminidr gemini_instruments gempy recipe_system"
+                        TMPDIR = "${env.WORKSPACE}/.tmp/ghost_integ/"
+                    }
+                    steps {
+                        echo "Running build #${env.BUILD_ID} on ${env.NODE_NAME}"
+                        checkout scm
+                        echo "${env.PATH}"
+                        sh '.jenkins/scripts/setup_dirs.sh'
+                        echo "GHOST tests"
+                        sh 'tox -e py312-ghost_integ -v -- --basetemp=${DRAGONS_TEST_OUT} --junit-xml reports/ghost_integ_results.xml ${TOX_ARGS}'
+                        echo "Reporting coverage"
+                        sh 'tox -e codecov -- -F ghost_integ'
+                    } // end steps
+                    post {
+                        always {
+                            junit (
+                                allowEmptyResults: true,
+                                testResults: '.tmp/py312-ghost_integ/reports/*_results.xml'
+                            )
+                            echo "Deleting GHOST Tests workspace ${env.WORKSPACE}"
+                            cleanWs()
+                            dir("${env.WORKSPACE}@tmp") {
+                              deleteDir()
+                            }
+                        }
+                    } // end post
+                } // end stage
             } // end parallel
         }
 

MANIFEST.in

@@ -4,7 +4,7 @@ include tox.ini
 include gempy/library/config/README
 
 recursive-include geminidr *.dat
-recursive-include geminidr *.fits *.html *.css *.js *.ico *.png *.xml *.svg *.json
+recursive-include geminidr *.fits *.fits.bz2 *.html *.css *.js *.ico *.png *.xml *.svg *.json
 recursive-include gempy *.c
 recursive-include gempy *.pyx
 recursive-include gempy/share/man/man1 *

astrodata/fits.py

@@ -682,7 +682,7 @@ def generate_boxes(shape, kernel):
         np.empty(shape, dtype=dtype),
         variance=np.zeros(shape, dtype=dtype) if with_uncertainty else None,
         mask=np.empty(shape, dtype=np.uint16) if with_mask else None,
-        meta=sequence[0].meta,
+        meta=deepcopy(sequence[0].meta),
         wcs=sequence[0].wcs,
     )
     # Delete other extensions because we don't know what to do with them

astrodata/testing.py

@@ -62,7 +62,7 @@ def assert_most_close(actual, desired, max_miss, rtol=1e-7, atol=0,
         if n_miss > max_miss:
             error_message = (
                     "%g mismatching elements are more than the " % n_miss +
-                    "expected %g." % max_miss +
+                    "expected %g.\n" % max_miss +
                     '\n'.join(e.args[0].split('\n')[3:]))
 
             raise AssertionError(error_message)
@@ -101,7 +101,7 @@ def assert_most_equal(actual, desired, max_miss, verbose=True):
         if n_miss > max_miss:
             error_message = (
                     "%g mismatching elements are more than the " % n_miss +
-                    "expected %g." % max_miss +
+                    "expected %g.\n" % max_miss +
                     '\n'.join(e.args[0].split('\n')[3:]))
 
             raise AssertionError(error_message)

gemini_instruments/gemini/adclass.py

@@ -2229,4 +2229,4 @@ def actual_central_wavelength(self, *args, **kwargs):
         This is not a descriptor. The args/kwargs accept whatever unit
         information central_wavelength() can handle.
         """
-        return self.central_wavelength(*args, **kwargs)
+        return self.central_wavelength(*args, **kwargs)

gemini_instruments/gnirs/adclass.py

@@ -7,7 +7,7 @@
 from ..common import build_group_id
 
 from .lookup import detector_properties, nominal_zeropoints, read_modes
-from .lookup import dispersion_by_config
+from .lookup import dispersion_by_config, xd_orders
 from .lookup import pixel_scale
 
 # NOTE: Temporary functions for test. gempy imports astrodata and
@@ -128,8 +128,11 @@ def dispersion(self):
             camera = 'Long'
         else:
             camera = None
-
-        filter = str(self.filter_name(pretty=True))[0]
+        if "XD" in self.tags:
+            order = self._grating_order()
+            filter = xd_orders.get(order, None)
+        else:
+            filter = str(self.filter_name(pretty=True))[0]
         dispersion = dispersion_by_config.get((grating, camera), {}).get(filter)
 
         if dispersion is None: