From f402995c6431054ad4d2982c894ce920839d3500 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 05:46:00 +0000 Subject: [PATCH 01/11] Bump lxml from 5.2.2 to 5.3.0 (#968) Bumps [lxml](https://github.com/lxml/lxml) from 5.2.2 to 5.3.0. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](https://github.com/lxml/lxml/compare/lxml-5.2.2...lxml-5.3.0) --- updated-dependencies: - dependency-name: lxml dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 638e6329c..9798fd6d0 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -1,6 +1,6 @@ importlib-metadata==6.8.0; python_version<'3.8' beautifulsoup4==4.12.3 -lxml==5.2.2 +lxml==5.3.0 Sphinx==7.3.7 sphinx-autoapi==3.1.2 From c335669be262810b3e53389c395d03c39242e303 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 05:50:57 +0000 Subject: [PATCH 02/11] Bump sphinx-autoapi from 3.1.2 to 3.3.2 (#969) Bumps [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) from 3.1.2 to 3.3.2. - [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases) - [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst) - [Commits](https://github.com/readthedocs/sphinx-autoapi/compare/v3.1.2...v3.3.2) --- updated-dependencies: - dependency-name: sphinx-autoapi dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 9798fd6d0..370167ba0 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -3,7 +3,7 @@ beautifulsoup4==4.12.3 lxml==5.3.0 Sphinx==7.3.7 -sphinx-autoapi==3.1.2 +sphinx-autoapi==3.3.2 sphinx-autobuild==2024.4.16 sphinx-book-theme==1.1.3 sphinx-design==0.6.0 From 7eb331f1ab7ba5c7177f14a54fbd7842b2947175 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 05:55:56 +0000 Subject: [PATCH 03/11] Update paramiko requirement from <3.4.1,>=3.0.0 to >=3.0.0,<3.5.1 (#971) Updates the requirements on [paramiko](https://github.com/paramiko/paramiko) to permit the latest version. - [Commits](https://github.com/paramiko/paramiko/compare/3.0.0...3.5.0) --- updated-dependencies: - dependency-name: paramiko dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_full.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_full.txt b/requirements_full.txt index 7899f2803..a448265d6 100644 --- a/requirements_full.txt +++ b/requirements_full.txt @@ -13,7 +13,7 @@ pyarrow>=14.0,<18.0 tables>=3.8,<5.0 openpyxl>=3.0.9,<3.2 jinja2>=3.0,<4 -paramiko>=3.0.0,<3.4.1 +paramiko>=3.0.0,<3.5.1 requests>=2.10,<3 redis>=5.0,<6 minio>=6.0,<8 From c614b719e0c7e697717d50c481b2fa675ec40d0b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 06:00:51 +0000 Subject: [PATCH 04/11] Bump myst-nb from 1.1.1 to 1.1.2 (#970) Bumps [myst-nb](https://github.com/executablebooks/myst-nb) from 1.1.1 to 1.1.2. - [Release notes](https://github.com/executablebooks/myst-nb/releases) - [Changelog](https://github.com/executablebooks/MyST-NB/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/myst-nb/compare/v1.1.1...v1.1.2) --- updated-dependencies: - dependency-name: myst-nb dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 370167ba0..c90643e2f 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -12,6 +12,6 @@ sphinx-toggleprompt==0.5.2 sphinx-copybutton==0.5.2 # does not work well with toggleprompt breathe==4.35.0 -myst-nb==1.1.1 +myst-nb==1.1.2 nbclient==0.10.0 docutils==0.21.2 From 6b88b6cdfe8c75b9ab3134052ee934feaca33230 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 06:05:57 +0000 Subject: [PATCH 05/11] Bump sphinx-autobuild from 2024.4.16 to 2024.10.3 (#974) Bumps [sphinx-autobuild](https://github.com/sphinx-doc/sphinx-autobuild) from 2024.4.16 to 2024.10.3. - [Release notes](https://github.com/sphinx-doc/sphinx-autobuild/releases) - [Changelog](https://github.com/sphinx-doc/sphinx-autobuild/blob/main/NEWS.rst) - [Commits](https://github.com/sphinx-doc/sphinx-autobuild/compare/2024.04.16...2024.10.03) --- updated-dependencies: - dependency-name: sphinx-autobuild dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index c90643e2f..ddc50c4fd 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -4,7 +4,7 @@ lxml==5.3.0 Sphinx==7.3.7 sphinx-autoapi==3.3.2 -sphinx-autobuild==2024.4.16 +sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-design==0.6.0 sphinxcontrib-plantuml==0.30 From de5889ac31ea129f048469826cd18306181c23e3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 06:10:56 +0000 Subject: [PATCH 06/11] Bump sphinx from 7.3.7 to 8.1.3 (#972) Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.3.7 to 8.1.3. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/v8.1.3/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.3.7...v8.1.3) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index ddc50c4fd..8a7e28e56 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -2,7 +2,7 @@ importlib-metadata==6.8.0; python_version<'3.8' beautifulsoup4==4.12.3 lxml==5.3.0 -Sphinx==7.3.7 +Sphinx==8.1.3 sphinx-autoapi==3.3.2 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 From 32b0aade9f4cb5729680ee358806044362dcf9b8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 21 Oct 2024 06:15:56 +0000 Subject: [PATCH 07/11] Bump sphinx-design from 0.6.0 to 0.6.1 (#973) Bumps [sphinx-design](https://github.com/executablebooks/sphinx-design) from 0.6.0 to 0.6.1. - [Release notes](https://github.com/executablebooks/sphinx-design/releases) - [Changelog](https://github.com/executablebooks/sphinx-design/blob/main/CHANGELOG.md) - [Commits](https://github.com/executablebooks/sphinx-design/compare/v0.6.0...v0.6.1) --- updated-dependencies: - dependency-name: sphinx-design dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 8a7e28e56..21c5c5111 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -6,7 +6,7 @@ Sphinx==8.1.3 sphinx-autoapi==3.3.2 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 -sphinx-design==0.6.0 +sphinx-design==0.6.1 sphinxcontrib-plantuml==0.30 sphinx-toggleprompt==0.5.2 sphinx-copybutton==0.5.2 # does not work well with toggleprompt From b6c8afd4fd0c549d4a9e4a7b00132fcfac6706f7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 28 Oct 2024 05:58:05 +0000 Subject: [PATCH 08/11] Bump sphinx-autoapi from 3.3.2 to 3.3.3 (#992) Bumps [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) from 3.3.2 to 3.3.3. - [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases) - [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst) - [Commits](https://github.com/readthedocs/sphinx-autoapi/compare/v3.3.2...v3.3.3) --- updated-dependencies: - dependency-name: sphinx-autoapi dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 21c5c5111..8b8177e40 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -3,7 +3,7 @@ beautifulsoup4==4.12.3 lxml==5.3.0 Sphinx==8.1.3 -sphinx-autoapi==3.3.2 +sphinx-autoapi==3.3.3 sphinx-autobuild==2024.10.3 sphinx-book-theme==1.1.3 sphinx-design==0.6.1 From c3a5419495d754e7912ba654bf5e53a69aaf460c Mon Sep 17 00:00:00 2001 From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com> Date: Thu, 31 Oct 2024 12:13:53 +0100 Subject: [PATCH 09/11] Update requirements_doc.txt --- requirements_doc.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_doc.txt b/requirements_doc.txt index 6784f8aa7..74b0f6ae5 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -1,6 +1,6 @@ importlib-metadata==6.8.0; python_version<'3.8' beautifulsoup4==4.12.3 -lxml==5.3.0 +breathe==4.35.0 docutils==0.21.2 lxml==5.3.0 myst-nb==1.1.2 From 922a89e0e9c7d3953c62b3440e162bff5cbd4764 Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Mon, 4 Nov 2024 13:58:57 +0100 Subject: [PATCH 10/11] Update bindings/python/dlite-jstore-python.i Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> --- bindings/python/dlite-jstore-python.i | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bindings/python/dlite-jstore-python.i b/bindings/python/dlite-jstore-python.i index 71c90da3c..ea68961ff 100644 --- a/bindings/python/dlite-jstore-python.i +++ b/bindings/python/dlite-jstore-python.i @@ -31,7 +31,7 @@ def format_dict( Notes: This method works with the dict-representation and does not - access instances. The only exception is when `d` correspond to + access instances. The only exception is when `d` corresponds to a data instance who's dimensions is a list of dimension lengths. In this case is the metadata needed to get dimension names. From d3bfbbd2ed83772e9af7ff389783f40d29e51372 Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Mon, 4 Nov 2024 14:06:29 +0100 Subject: [PATCH 11/11] Added comments about equal soft7 and old representations --- bindings/python/tests/test_jstore.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/bindings/python/tests/test_jstore.py b/bindings/python/tests/test_jstore.py index ace0476f6..2f543f4bf 100644 --- a/bindings/python/tests/test_jstore.py +++ b/bindings/python/tests/test_jstore.py @@ -14,7 +14,7 @@ # Test format_dict(), arg: soft7 -D1 = { +D1 = { # soft7 representation "uri": "http://onto-ns.com/meta/ex/0.2/Test", "dimensions": {"n": "number of something"}, "properties": { @@ -22,7 +22,7 @@ "b": {"type": "float64", "shape": ["n"]}, }, } -D2 = { +D2 = { # old (array) representation "uri": "http://onto-ns.com/meta/ex/0.2/Test", "dimensions": [{"name": "n", "description": "number of something"}], "properties": [ @@ -35,6 +35,8 @@ assert dlite.format_dict(D2, soft7=True) == D1 assert dlite.format_dict(D2, soft7=False) == D2 +# soft7 representation. This is identical to the old representation for +# data instances d1 = { "uuid": "d6a1c1db-44b6-5b87-b815-83f1127395b6", "meta": "http://onto-ns.com/meta/ex/0.2/Test", @@ -44,7 +46,7 @@ "b": [1.1, 2.2, 3.3], }, } -d2 = { +d2 = { # old representation "uuid": "d6a1c1db-44b6-5b87-b815-83f1127395b6", "meta": "http://onto-ns.com/meta/ex/0.2/Test", "dimensions": {"n": 3},