Change POD default rtol and fix analyze_pickle demo for numpy master

.binder/Dockerfile

@@ -5,7 +5,7 @@
 # the container, local dev needs it in path from mounted src
 # we trick docker into fulfilling both roles via a conditional ONBUILD
 # if you want to use the local dev setup, see docker/docker-compose.yml
-ARG BASE=pymor/jupyter_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+ARG BASE=pymor/jupyter_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
 ARG BUILD_ENV=binder
 
 FROM $BASE as image_binder

.ci/gitlab/ci.yml

@@ -20,8 +20,8 @@ stages:
     except:
         - /^staging/.*$/i
     variables:
-        PYPI_MIRROR_TAG: b59ac79e36381fb509ec5a90cfaae5cec4be3a60
-        CI_IMAGE_TAG: b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        PYPI_MIRROR_TAG: d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
+        CI_IMAGE_TAG: d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
         PYMOR_HYPOTHESIS_PROFILE: ci
 
 .pytest:
@@ -139,7 +139,7 @@ stages:
 
 .sanity_checks:
     extends: .test_base
-    image: pymor/ci_sanity:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/ci_sanity:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     stage: sanity
 #******** end definition of base jobs *********************************************************************************#
 
@@ -164,18 +164,18 @@ minimal_cpp_demo:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script: ./.ci/gitlab/cpp_demo.bash
 mpi 3 6:
     extends: .pytest
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -191,9 +191,9 @@ mpi 3 7:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -209,9 +209,9 @@ mpi 3 8:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -227,9 +227,9 @@ notebooks_dir 3 6:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -245,9 +245,9 @@ notebooks_dir 3 7:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -263,9 +263,9 @@ notebooks_dir 3 8:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -281,9 +281,9 @@ pip_installed 3 6:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -299,9 +299,9 @@ pip_installed 3 7:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -317,9 +317,9 @@ pip_installed 3 8:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -335,9 +335,9 @@ vanilla 3 6:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -353,9 +353,9 @@ vanilla 3 7:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -371,9 +371,9 @@ vanilla 3 8:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -389,9 +389,9 @@ numpy_git 3 8:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -407,9 +407,9 @@ oldest 3 6:
     except:
         - schedules
     services:
-        - name: pymor/pypi-mirror_oldest_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_oldest_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
     script:
         - |
           if [[ "$CI_COMMIT_REF_NAME" == *"github/"* ]]; then
@@ -426,9 +426,9 @@ ci_weekly 3 6:
     only:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.6:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.6:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
 
     script: ./.ci/gitlab/test_vanilla.bash
 ci_weekly 3 7:
@@ -437,9 +437,9 @@ ci_weekly 3 7:
     only:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.7:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.7:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
 
     script: ./.ci/gitlab/test_vanilla.bash
 ci_weekly 3 8:
@@ -448,9 +448,9 @@ ci_weekly 3 8:
     only:
         - schedules
     services:
-        - name: pymor/pypi-mirror_stable_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+        - name: pymor/pypi-mirror_stable_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
           alias: pypi_mirror
-    image: pymor/testing_py3.8:b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+    image: pymor/testing_py3.8:d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
 
     script: ./.ci/gitlab/test_vanilla.bash
 submit vanilla 3 6:

.ci/gitlab/test_pip_installed.bash

@@ -12,7 +12,12 @@ PIP_CLONE_URL="git+${CI_PROJECT_URL}@${CI_COMMIT_SHA}"
 # source /tmp/venv/bin/activate
 pip install ${PIP_CLONE_URL}
 pip uninstall -y pymor
-pip install ${PIP_CLONE_URL}#egg=pymor[full]
+
+# this is currently disabled because it erroneously pulls in pyqt5
+# pip install ${PIP_CLONE_URL}#egg=pymor[full]
+# pip uninstall -y pymor
+
+pip install .[full]
 pip uninstall -y pymor
 # other requirements are installed from pymor[full]
 pip install -r requirements-ci.txt

.env

@@ -2,6 +2,6 @@ DOCKER_BASE_PYTHON=3.7
 PYMOR_TEST_SCRIPT=vanilla
 PYPI_MIRROR=stable
 PYMOR_TEST_OS=debian_buster
-PYPI_MIRROR_TAG=b59ac79e36381fb509ec5a90cfaae5cec4be3a60
-CI_IMAGE_TAG=b59ac79e36381fb509ec5a90cfaae5cec4be3a60
+PYPI_MIRROR_TAG=d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
+CI_IMAGE_TAG=d4cc6ff37b42c8c36d1a4d533399d28fa6c5edb2
 PYMOR_HYPOTHESIS_PROFILE=dev

src/pymor/algorithms/pod.py

@@ -15,7 +15,7 @@
 
 
 @defaults('rtol', 'atol', 'l2_err', 'method', 'orth_tol')
-def pod(A, product=None, modes=None, rtol=4e-8, atol=0., l2_err=0.,
+def pod(A, product=None, modes=None, rtol=1e-7, atol=0., l2_err=0.,
         method='method_of_snapshots', orth_tol=1e-10):
     """Proper orthogonal decomposition of `A`.
 

src/pymor/algorithms/svd_va.py

@@ -15,7 +15,7 @@
 
 
 @defaults('rtol', 'atol', 'l2_err')
-def method_of_snapshots(A, product=None, modes=None, rtol=4e-8, atol=0., l2_err=0.):
+def method_of_snapshots(A, product=None, modes=None, rtol=1e-7, atol=0., l2_err=0.):
     """SVD of a |VectorArray| using the method of snapshots.
 
     Viewing the |VectorArray| `A` as a `A.dim` x `len(A)` matrix, the

src/pymordemos/analyze_pickle.py

@@ -115,8 +115,8 @@ def analyze_pickle_histogram(args):
         axHisty = plt.axes(rect_histy)
 
         # scatter plot
-        total_min = min(min(ests), min(errs)) * 0.9
-        total_max = max(max(ests), max(errs)) * 1.1
+        total_min = min(np.min(ests), np.min(errs)) * 0.9
+        total_max = max(np.max(ests), np.max(errs)) * 1.1
         axScatter.set_xscale('log')
         axScatter.set_yscale('log')
         axScatter.set_xlim([total_min, total_max])
@@ -137,15 +137,15 @@ def analyze_pickle_histogram(args):
         axHisty.set_yticklabels([])
         axHistx.set_xlim(axScatter.get_xlim())
         axHisty.set_ylim(axScatter.get_ylim())
-        axHistx.set_ylim([0, max(max(x_hist), max(y_hist))])
-        axHisty.set_xlim([0, max(max(x_hist), max(y_hist))])
+        axHistx.set_ylim([0, max(np.max(x_hist), np.max(y_hist))])
+        axHisty.set_xlim([0, max(np.max(x_hist), np.max(y_hist))])
 
         plt.show()
 
     elif hasattr(rom, 'estimate'):
 
-        total_min = min(ests) * 0.9
-        total_max = max(ests) * 1.1
+        total_min = np.min(ests) * 0.9
+        total_max = np.max(ests) * 1.1
 
         hist, bin_edges = np.histogram(ests, bins=_bins(total_min, total_max))
         plt.bar(bin_edges[1:], hist, width=bin_edges[:-1] - bin_edges[1:], color='blue')
@@ -157,8 +157,8 @@ def analyze_pickle_histogram(args):
 
     elif args['--detailed']:
 
-        total_min = min(ests) * 0.9
-        total_max = max(ests) * 1.1
+        total_min = np.min(ests) * 0.9
+        total_max = np.max(ests) * 1.1
 
         hist, bin_edges = np.histogram(errs, bins=_bins(total_min, total_max))
         plt.bar(bin_edges[1:], hist, width=bin_edges[:-1] - bin_edges[1:], color='blue')

src/pymortests/algorithms/basic.py

@@ -196,14 +196,13 @@ def test_almost_equal_incompatible(vector_arrays):
 
 @given(pyst.base_vector_arrays(count=2))
 @settings(deadline=None)
-def test_project_array(bases):
-    U = bases[0][:-2]
-    basis = bases[1]
+def test_project_array(arrays):
+    U, basis = arrays
     U_p = project_array(U, basis, orthonormal=False)
     onb = gram_schmidt(basis)
     U_p2 = project_array(U, onb, orthonormal=True)
     err = relative_error(U_p, U_p2)
-    tol = 3e-10
+    tol = np.finfo(np.float64).eps * np.linalg.cond(basis.gramian()) * 100.
     assert np.all(err < tol)
 
 

src/pymortests/strategies.py

@@ -382,7 +382,7 @@ def base_vector_arrays(draw, count=1, dtype=None, max_dim=100):
     length = space.dim
 
     # this lets hypothesis control np's random state too
-    random = draw(hyst.randoms())
+    random = draw(hyst.random_module())
     # scipy performs this check although technically numpy accepts a different range
     assume(0 <= random.seed < 2**32 - 1)
     random_correlation = random_correlation_gen(random.seed)