From 6da26299185abda7dccadc3a9366cd46fe63a7ec Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:12:17 +0100 Subject: [PATCH 01/16] Test oldest dependencies --- .github/workflows/test.yml | 4 ++++ tox.ini | 29 +++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8181681dc7a..719ab8c5ec6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -45,6 +45,10 @@ jobs: python-version: 3.8 tox_env: orange-latest name: Latest + - os: ubuntu-18.04 + python-version: 3.7 + tox_env: orange-oldest + name: Oldest dependencies services: postgres: diff --git a/tox.ini b/tox.ini index 3f37432e53f..ccf0c1eb562 100644 --- a/tox.ini +++ b/tox.ini @@ -38,6 +38,35 @@ deps = latest: https://github.com/pyqtgraph/pyqtgraph/archive/refs/heads/master.zip#egg=pyqtgraph latest: https://github.com/biolab/orange-canvas-core/archive/refs/heads/master.zip#egg=orange-canvas-core latest: https://github.com/biolab/orange-widget-base/archive/refs/heads/master.zip#egg=orange-widget-base + oldest: orange-canvas-core==0.1.24 + oldest: orange-widget-base==4.16.1 + oldest: AnyQt==0.0.11 + oldest: pyqtgraph==0.11.1 + oldest: matplotlib==2.0.0 + oldest: qtconsole==4.7.2 + oldest: pygments==2.8.0 + oldest: pip==9.0 + oldest: numpy==1.16.0 + oldest: scipy==0.16.1 + oldest: scikit-learn==0.23.1 + oldest: bottleneck==1.0.0 + oldest: xlrd==0.9.2 + # oldest: xlsxwriter + oldest: chardet==3.0.2 + oldest: joblib==0.9.4 + # oldest: keyring + # oldest: keyrings.alt + oldest: setuptools==36.3 + # oldest: serverfiles + # oldest: networkx + oldest: python-louvain==0.13 + # oldest: requests + oldest: openTSNE==0.6.1 + oldest: baycomp==1.0.2 + oldest: pandas==1.3.0 + # oldest: pyyaml + # oldest: openpyxl + oldest: httpx==0.14.0 commands_pre = # Verify installed packages have compatible dependencies From 453e64d30f9c5570de2966ce693a994c1ed9d904 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:22:21 +0100 Subject: [PATCH 02/16] orange-canvas-core 0.1.24 depends on pip>=18.0 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 549c349e630..f4d1a34a276 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,4 +1,4 @@ -pip>=9.0 +pip>=18.0 numpy>=1.16.0 scipy>=0.16.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost diff --git a/tox.ini b/tox.ini index ccf0c1eb562..e9faf71d80e 100644 --- a/tox.ini +++ b/tox.ini @@ -45,7 +45,7 @@ deps = oldest: matplotlib==2.0.0 oldest: qtconsole==4.7.2 oldest: pygments==2.8.0 - oldest: pip==9.0 + oldest: pip==18.0 oldest: numpy==1.16.0 oldest: scipy==0.16.1 oldest: scikit-learn==0.23.1 From c16045912177dbb9d1ee9ee065331dc8f7a20892 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:31:09 +0100 Subject: [PATCH 03/16] orange-canvas-core 0.1.24 depends on AnyQt>=0.0.13 --- requirements-gui.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-gui.txt b/requirements-gui.txt index aa44a6d91dd..b24f3968827 100644 --- a/requirements-gui.txt +++ b/requirements-gui.txt @@ -1,7 +1,7 @@ orange-canvas-core>=0.1.24,<0.2a orange-widget-base>=4.16.1 -AnyQt>=0.0.11 +AnyQt>=0.0.13 pyqtgraph>=0.11.1 matplotlib>=2.0.0 diff --git a/tox.ini b/tox.ini index e9faf71d80e..95cd581ce4b 100644 --- a/tox.ini +++ b/tox.ini @@ -40,7 +40,7 @@ deps = latest: https://github.com/biolab/orange-widget-base/archive/refs/heads/master.zip#egg=orange-widget-base oldest: orange-canvas-core==0.1.24 oldest: orange-widget-base==4.16.1 - oldest: AnyQt==0.0.11 + oldest: AnyQt==0.0.13 oldest: pyqtgraph==0.11.1 oldest: matplotlib==2.0.0 oldest: qtconsole==4.7.2 From 48395f5e9f1cc8c243e8cca224f8a1adfc67390b Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:37:34 +0100 Subject: [PATCH 04/16] scikit-learn 0.23.1 depends on scipy>=0.19.1 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index f4d1a34a276..2277b2cf863 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,6 +1,6 @@ pip>=18.0 numpy>=1.16.0 -scipy>=0.16.1 +scipy>=0.19.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 diff --git a/tox.ini b/tox.ini index 95cd581ce4b..0cbdf311aab 100644 --- a/tox.ini +++ b/tox.ini @@ -47,7 +47,7 @@ deps = oldest: pygments==2.8.0 oldest: pip==18.0 oldest: numpy==1.16.0 - oldest: scipy==0.16.1 + oldest: scipy==0.19.1 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.0.0 oldest: xlrd==0.9.2 From a61d009934e49d132d83109f5bb3d7ffbfc14fe2 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:39:23 +0100 Subject: [PATCH 05/16] baycomp 1.0.2 depends on matplotlib>=2.1.2 --- requirements-gui.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-gui.txt b/requirements-gui.txt index b24f3968827..d66a0babc05 100644 --- a/requirements-gui.txt +++ b/requirements-gui.txt @@ -4,6 +4,6 @@ orange-widget-base>=4.16.1 AnyQt>=0.0.13 pyqtgraph>=0.11.1 -matplotlib>=2.0.0 +matplotlib>=2.1.2 qtconsole>=4.7.2 pygments>=2.8.0 diff --git a/tox.ini b/tox.ini index 0cbdf311aab..d1ad7c66391 100644 --- a/tox.ini +++ b/tox.ini @@ -42,7 +42,7 @@ deps = oldest: orange-widget-base==4.16.1 oldest: AnyQt==0.0.13 oldest: pyqtgraph==0.11.1 - oldest: matplotlib==2.0.0 + oldest: matplotlib==2.1.2 oldest: qtconsole==4.7.2 oldest: pygments==2.8.0 oldest: pip==18.0 From 44a7bb373c4736503f3b1d2725184fdbcfda3c3e Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:51:51 +0100 Subject: [PATCH 06/16] Increment matplotlib to an easily testable version --- requirements-gui.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-gui.txt b/requirements-gui.txt index d66a0babc05..50cfb83aa10 100644 --- a/requirements-gui.txt +++ b/requirements-gui.txt @@ -4,6 +4,6 @@ orange-widget-base>=4.16.1 AnyQt>=0.0.13 pyqtgraph>=0.11.1 -matplotlib>=2.1.2 +matplotlib>=2.2.5 qtconsole>=4.7.2 pygments>=2.8.0 diff --git a/tox.ini b/tox.ini index d1ad7c66391..fc05c3016ec 100644 --- a/tox.ini +++ b/tox.ini @@ -42,7 +42,7 @@ deps = oldest: orange-widget-base==4.16.1 oldest: AnyQt==0.0.13 oldest: pyqtgraph==0.11.1 - oldest: matplotlib==2.1.2 + oldest: matplotlib==2.2.5 oldest: qtconsole==4.7.2 oldest: pygments==2.8.0 oldest: pip==18.0 From 3e75db5223a6ffa760d82b4992f7807ff9d381b7 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 13:57:05 +0100 Subject: [PATCH 07/16] scikit-learn 0.23.1 depends on joblib>=0.11 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 2277b2cf863..6a053ce5c75 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -12,7 +12,7 @@ xlsxwriter # Encoding detection chardet>=3.0.2 # Multiprocessing abstraction -joblib>=0.9.4 +joblib>=0.11 keyring keyrings.alt # for alternative keyring implementations setuptools>=36.3 diff --git a/tox.ini b/tox.ini index fc05c3016ec..9e4ba0fa00b 100644 --- a/tox.ini +++ b/tox.ini @@ -53,7 +53,7 @@ deps = oldest: xlrd==0.9.2 # oldest: xlsxwriter oldest: chardet==3.0.2 - oldest: joblib==0.9.4 + oldest: joblib==0.11 # oldest: keyring # oldest: keyrings.alt oldest: setuptools==36.3 From a5be5df5a68ef3211e459c65d112cf315da955fe Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 15:52:42 +0100 Subject: [PATCH 08/16] opentsne 0.6.1 depends on numpy>=1.16.6 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 6a053ce5c75..e0db0709f89 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,5 +1,5 @@ pip>=18.0 -numpy>=1.16.0 +numpy>=1.16.6 scipy>=0.19.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 diff --git a/tox.ini b/tox.ini index 9e4ba0fa00b..af3575c6c7b 100644 --- a/tox.ini +++ b/tox.ini @@ -46,7 +46,7 @@ deps = oldest: qtconsole==4.7.2 oldest: pygments==2.8.0 oldest: pip==18.0 - oldest: numpy==1.16.0 + oldest: numpy==1.16.6 oldest: scipy==0.19.1 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.0.0 From 2b5212fdb5ba038915d45462737a4e423c711b5f Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 16:00:47 +0100 Subject: [PATCH 09/16] pandas 1.3.0 depends on numpy>=1.17.3 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index e0db0709f89..80e92a7d604 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,5 +1,5 @@ pip>=18.0 -numpy>=1.16.6 +numpy>=1.17.3 scipy>=0.19.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 diff --git a/tox.ini b/tox.ini index af3575c6c7b..0b99f63e7a9 100644 --- a/tox.ini +++ b/tox.ini @@ -46,7 +46,7 @@ deps = oldest: qtconsole==4.7.2 oldest: pygments==2.8.0 oldest: pip==18.0 - oldest: numpy==1.16.6 + oldest: numpy==1.17.3 oldest: scipy==0.19.1 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.0.0 From 7b72768f8047729d8c9490b31480129771b3e64e Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 16:07:05 +0100 Subject: [PATCH 10/16] Increment scipy to an easily testable version --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 80e92a7d604..a6c6cfafb82 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,6 +1,6 @@ pip>=18.0 numpy>=1.17.3 -scipy>=0.19.1 +scipy>=1.1.0 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 diff --git a/tox.ini b/tox.ini index 0b99f63e7a9..84e9fc67df2 100644 --- a/tox.ini +++ b/tox.ini @@ -47,7 +47,7 @@ deps = oldest: pygments==2.8.0 oldest: pip==18.0 oldest: numpy==1.17.3 - oldest: scipy==0.19.1 + oldest: scipy==1.1.0 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.0.0 oldest: xlrd==0.9.2 From 4f2860bf5ba5ce90438b6b6e9d60149a7c4c6984 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 16:18:36 +0100 Subject: [PATCH 11/16] Require bottleneck 1.2.1 due to build problems with 1.0.0 --- requirements-core.txt | 1 - tox.ini | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index a6c6cfafb82..eb1a635e19f 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -4,7 +4,6 @@ scipy>=1.1.0 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 -bottleneck>=1.0.0 # Reading Excel files xlrd>=0.9.2 # Writing Excel Files diff --git a/tox.ini b/tox.ini index 84e9fc67df2..4933a21cae8 100644 --- a/tox.ini +++ b/tox.ini @@ -49,7 +49,7 @@ deps = oldest: numpy==1.17.3 oldest: scipy==1.1.0 oldest: scikit-learn==0.23.1 - oldest: bottleneck==1.0.0 + oldest: bottleneck==1.2.1 oldest: xlrd==0.9.2 # oldest: xlsxwriter oldest: chardet==3.0.2 From 0d6b5c4f347771c713a789c9a9b183e50865e7a9 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 17:39:27 +0100 Subject: [PATCH 12/16] Require bottleneck 1.3.2 --- requirements-core.txt | 1 + tox.ini | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements-core.txt b/requirements-core.txt index eb1a635e19f..58ed4d34185 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -4,6 +4,7 @@ scipy>=1.1.0 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 +bottleneck>=1.3.2 # Reading Excel files xlrd>=0.9.2 # Writing Excel Files diff --git a/tox.ini b/tox.ini index 4933a21cae8..db9315ff298 100644 --- a/tox.ini +++ b/tox.ini @@ -49,7 +49,7 @@ deps = oldest: numpy==1.17.3 oldest: scipy==1.1.0 oldest: scikit-learn==0.23.1 - oldest: bottleneck==1.2.1 + oldest: bottleneck==1.3.2 oldest: xlrd==0.9.2 # oldest: xlsxwriter oldest: chardet==3.0.2 From 89143ab32e72d126f2eb4d575d2b18554941b412 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 18:01:45 +0100 Subject: [PATCH 13/16] Pandas requires version '1.2.0' or newer of 'scipy' (version '1.1.0' currently installed) --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 58ed4d34185..94703c77231 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,6 +1,6 @@ pip>=18.0 numpy>=1.17.3 -scipy>=1.1.0 +scipy>=1.2.0 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 diff --git a/tox.ini b/tox.ini index db9315ff298..5eed2623863 100644 --- a/tox.ini +++ b/tox.ini @@ -47,7 +47,7 @@ deps = oldest: pygments==2.8.0 oldest: pip==18.0 oldest: numpy==1.17.3 - oldest: scipy==1.1.0 + oldest: scipy==1.2.0 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.3.2 oldest: xlrd==0.9.2 From 6ab2e656baac59459c735c72c5d1285520c0cf8e Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Thu, 13 Jan 2022 19:06:19 +0100 Subject: [PATCH 14/16] test_gb_cls and test_gb_reg require scipy 1.3.1 --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index 94703c77231..cc389857770 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -1,6 +1,6 @@ pip>=18.0 numpy>=1.17.3 -scipy>=1.2.0 +scipy>=1.3.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 scikit-learn>1.0.0 diff --git a/tox.ini b/tox.ini index 5eed2623863..68e97fa9029 100644 --- a/tox.ini +++ b/tox.ini @@ -47,7 +47,7 @@ deps = oldest: pygments==2.8.0 oldest: pip==18.0 oldest: numpy==1.17.3 - oldest: scipy==1.2.0 + oldest: scipy==1.3.1 oldest: scikit-learn==0.23.1 oldest: bottleneck==1.3.2 oldest: xlrd==0.9.2 From e34bf564de0be010e67dec2fe014b6c67bf0ee9e Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Fri, 14 Jan 2022 12:26:22 +0100 Subject: [PATCH 15/16] Update oldest test according to dependencies --- requirements-core.txt | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements-core.txt b/requirements-core.txt index cc389857770..1aef14469f5 100644 --- a/requirements-core.txt +++ b/requirements-core.txt @@ -3,7 +3,7 @@ numpy>=1.17.3 scipy>=1.3.1 # scikit-learn version 1.0.0 includes problematic libomp 12 which breaks xgboost # https://github.com/scikit-learn/scikit-learn/pull/21227 -scikit-learn>1.0.0 +scikit-learn>=1.0.1 bottleneck>=1.3.2 # Reading Excel files xlrd>=0.9.2 diff --git a/tox.ini b/tox.ini index 68e97fa9029..b62d5e4b12e 100644 --- a/tox.ini +++ b/tox.ini @@ -48,7 +48,7 @@ deps = oldest: pip==18.0 oldest: numpy==1.17.3 oldest: scipy==1.3.1 - oldest: scikit-learn==0.23.1 + oldest: scikit-learn==1.0.1 oldest: bottleneck==1.3.2 oldest: xlrd==0.9.2 # oldest: xlsxwriter From 5a0c8dbc568720d15ec2452a0efc5fe6dabbc593 Mon Sep 17 00:00:00 2001 From: Marko Toplak Date: Fri, 14 Jan 2022 12:34:08 +0100 Subject: [PATCH 16/16] Update meta.yaml requirements --- conda-recipe/meta.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 50d0aa06f3a..ba72fa88f69 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -38,32 +38,32 @@ requirements: run: - python - setuptools >=36.3 - - numpy >=1.16.0 - - scipy >=0.16.1 - - scikit-learn >0.23.0 - - bottleneck >=1.0.0 + - numpy >=1.17.3 + - scipy >=1.3.1 + - scikit-learn >=1.0.1 + - bottleneck >=1.3.2 - chardet >=3.0.2 - xlrd >=0.9.2 - xlsxwriter - - anyqt >=0.0.11 - - pyqt >=5.12,!=5.15.1 + - anyqt >=0.0.13 + - pyqt >=5.12,!=5.15.1,<6.0 - pyqtgraph >=0.11.1 - - joblib >=0.9.4 + - joblib >=0.11 - keyring - keyrings.alt - - pip >=9.0 + - pip >=18.0 - python.app # [osx] - serverfiles - python-louvain >=0.13 - requests - - matplotlib-base >=2.0.0 + - matplotlib-base >=2.2.5 - openTSNE >=0.6.1 - - pandas >=1.1.0 + - pandas >=1.3.0 - pyyaml - orange-canvas-core >=0.1.24,<0.2a - orange-widget-base >=4.16.1 - openpyxl - - httpx >=0.14 + - httpx >=0.14,<0.20 - baycomp >=1.0.2 # cachecontrol (required by canvas core) <0.12.5 is incompatible with msgpack 1.0 - cachecontrol >=0.12.6