From 6546e08f96cd3c5ea39468c506a8745d98922e09 Mon Sep 17 00:00:00 2001 From: veenstrajelmer <60435591+veenstrajelmer@users.noreply.github.com> Date: Thu, 4 Jul 2024 11:07:32 +0200 Subject: [PATCH 01/48] update numpy version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bf984f23d..0611992fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ python = "^3.8" netCDF4 = "^1.5" numpy = [ { version = "^1.21", python = "^3.8" }, - { version = "^1.26", python = "^3.12" } + { version = "^2.0.0", python = "^3.12" } ] pydantic = "^2.5" lxml = "^4.6" From 2e58badd08cf015d3839f332592f81b5d880da7c Mon Sep 17 00:00:00 2001 From: veenstrajelmer <60435591+veenstrajelmer@users.noreply.github.com> Date: Thu, 4 Jul 2024 11:08:28 +0200 Subject: [PATCH 02/48] deleted poetry.lock --- poetry.lock | 3934 --------------------------------------------------- 1 file changed, 3934 deletions(-) delete mode 100644 poetry.lock diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 2c72db166..000000000 --- a/poetry.lock +++ /dev/null @@ -1,3934 +0,0 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. - 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{ version = "^2.0.0", python = "^3.12" } + { version = ">=1.26", python = "^3.12" } ] pydantic = "^2.5" lxml = "^4.6" From dbbe8e1940181332234ec5afd16ee9c8cef2961f Mon Sep 17 00:00:00 2001 From: veenstrajelmer <60435591+veenstrajelmer@users.noreply.github.com> Date: Thu, 4 Jul 2024 11:13:22 +0200 Subject: [PATCH 04/48] dropped py3.8 support to let poetry resolve properly --- pyproject.toml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2bd6b05e2..99cc39c09 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,12 +14,9 @@ homepage = "https://deltares.github.io/HYDROLIB-core" "issue tracker" = "https://github.com/Deltares/HYDROLIB-core/issues" [tool.poetry.dependencies] -python = "^3.8" +python = "^3.9" netCDF4 = "^1.5" -numpy = [ - { version = "^1.21", python = "^3.8" }, - { version = ">=1.26", python = "^3.12" } -] +numpy = "^2.0.0" pydantic = "^2.5" lxml = "^4.6" meshkernel = "^4.1.0" From a0aeccffb07763a05ca33c8c5546d02be22e61d1 Mon Sep 17 00:00:00 2001 From: veenstrajelmer <60435591+veenstrajelmer@users.noreply.github.com> Date: Thu, 4 Jul 2024 12:02:11 +0200 Subject: [PATCH 05/48] numpy 1.25 for all python versions --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 99cc39c09..8311cebdf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ homepage = "https://deltares.github.io/HYDROLIB-core" [tool.poetry.dependencies] python = "^3.9" netCDF4 = "^1.5" -numpy = "^2.0.0" +numpy = "^1.25" pydantic = "^2.5" lxml = "^4.6" meshkernel = "^4.1.0" From 24edfba1859c4504c122b9a4107e7d677c20bdd6 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 11:42:03 +0200 Subject: [PATCH 06/48] loosen netcdf4 requirements --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 214b0bc2a..ed2b3e4b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,10 +15,10 @@ homepage = "https://deltares.github.io/HYDROLIB-core" [tool.poetry.dependencies] python = "^3.8" -netCDF4 = "^1.5,!=1.7.*" +netCDF4 = "^1.5" numpy = [ - 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So no caret requirement here. numpy = [ - { version = ">=1.21", python = "^3.8" }, - { version = "^2", python = "^3.12" } + { version = ">=1.24", python = "3.8" }, + { version = ">=1.25", python = "^3.9" } ] pydantic = "^2.5" lxml = "^4.6" From f9d21b0d6269b69e4d6bc2f962e394e6df861eb3 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 11:58:16 +0200 Subject: [PATCH 09/48] numpy 2 test --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a980a21f0..9f1689521 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ netCDF4 = [ # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. numpy = [ { version = ">=1.24", python = "3.8" }, - { version = ">=1.25", python = "^3.9" } + { version = ">=2.0", python = "^3.9" } ] pydantic = "^2.5" lxml = "^4.6" From 0776a84f8d31fe9ce315b3e7604212c86d7d3643 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 12:10:42 +0200 Subject: [PATCH 10/48] lowered numpy and updated lockfile --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9f1689521..a980a21f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ netCDF4 = [ # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. numpy = [ { version = ">=1.24", python = "3.8" }, - { version = ">=2.0", python = "^3.9" } + { version = ">=1.25", python = "^3.9" } ] pydantic = "^2.5" lxml = "^4.6" From e9bb086672bc77feefbe066552310984e0872c94 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 12:14:28 +0200 Subject: [PATCH 11/48] simplified version specifications --- pyproject.toml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a980a21f0..09e524523 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,16 +15,9 @@ homepage = "https://deltares.github.io/HYDROLIB-core" [tool.poetry.dependencies] python = "^3.8" -# exclude netcdf 1.7 to avoid issues with python 3.8 on windows -netCDF4 = [ - { version = "^1.5,!=1.7.*", python = "3.8" }, - { version = "^1.5", python = "^3.9" } -] +netCDF4 = "^1.5" # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. -numpy = [ - { version = ">=1.24", python = "3.8" }, - { version = ">=1.25", python = "^3.9" } -] +numpy = ">=1.24" pydantic = "^2.5" lxml = "^4.6" meshkernel = "^4.2.0" From 453124e3b6a6aefc18d87fb671c80a7942334323 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 12:28:01 +0200 Subject: [PATCH 12/48] updated deps --- poetry.lock | 4291 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 11 +- 2 files changed, 4300 insertions(+), 2 deletions(-) create mode 100644 poetry.lock diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..45c4f645e --- /dev/null +++ b/poetry.lock @@ -0,0 +1,4291 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = 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= [ - { version = "^1.5,!=1.7.*", python = "3.8" }, - { version = "^1.5", python = "^3.9" } -] +netCDF4 = "^1.5" # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. -numpy = [ - { version = ">=1.24", python = "3.8" }, - { version = ">=1.25", python = "^3.9" } -] +numpy = ">=1.24" pydantic = "^2.5" lxml = ">=4.6" meshkernel = "^4.2.0" From ced944c1322c1193fba16b491326d7dee9473b79 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 15:40:50 +0200 Subject: [PATCH 16/48] renable python 3.8 to test --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 42953f87a..f9c9a9e6c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ homepage = "https://deltares.github.io/HYDROLIB-core" "issue tracker" = "https://github.com/Deltares/HYDROLIB-core/issues" [tool.poetry.dependencies] -python = "^3.9" +python = "^3.8" # exclude netcdf 1.7 to avoid issues with python 3.8 on windows netCDF4 = "^1.5" # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. From df4a8420ac2f3947b402fa69f2f3c3ff086ae18f Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 15:42:50 +0200 Subject: [PATCH 17/48] revert --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f9c9a9e6c..42953f87a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ homepage = "https://deltares.github.io/HYDROLIB-core" "issue tracker" = "https://github.com/Deltares/HYDROLIB-core/issues" [tool.poetry.dependencies] -python = "^3.8" +python = "^3.9" # exclude netcdf 1.7 to avoid issues with python 3.8 on windows netCDF4 = "^1.5" # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. From 23f7e88e609cb06011fea1aa1e106330190a61ee Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 15:48:53 +0200 Subject: [PATCH 18/48] python 3.8 again --- poetry.lock | 6 +++--- pyproject.toml | 12 +++++++++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 93eb72aa2..c68a9f24c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -426,8 +426,8 @@ files = [ [package.dependencies] numpy = [ - {version = ">1.13.3", markers = "python_version < \"3.12.0.rc1\""}, {version = ">=1.26.0b1", markers = "python_version >= \"3.12.0.rc1\""}, + {version = ">1.13.3", markers = "python_version < \"3.12.0.rc1\""}, ] [[package]] @@ -2699,9 +2699,9 @@ files = [ [package.dependencies] numpy = [ + {version = ">=1.26.0", markers = "python_version >= \"3.12\""}, {version = ">=1.22.4", markers = "python_version < \"3.11\""}, {version = ">=1.23.2", markers = "python_version == \"3.11\""}, - {version = ">=1.26.0", markers = "python_version >= \"3.12\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -3041,8 +3041,8 @@ files = [ annotated-types = ">=0.6.0" pydantic-core = "2.23.4" typing-extensions = [ - {version = ">=4.6.1", markers = "python_version < \"3.13\""}, {version = ">=4.12.2", markers = "python_version >= \"3.13\""}, + {version = ">=4.6.1", markers = "python_version < \"3.13\""}, ] [package.extras] diff --git a/pyproject.toml b/pyproject.toml index 42953f87a..c178e56ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,11 +14,17 @@ homepage = "https://deltares.github.io/HYDROLIB-core" "issue tracker" = "https://github.com/Deltares/HYDROLIB-core/issues" [tool.poetry.dependencies] -python = "^3.9" +python = "^3.8" # exclude netcdf 1.7 to avoid issues with python 3.8 on windows -netCDF4 = "^1.5" +netCDF4 = [ + { version = "^1.5,!=1.7.*", python = "3.8" }, + { version = "^1.5", python = "^3.9" } +] # for future python 3.13 support we need to allow numpy v2 and numpy v1 is also still widely uses. So no caret requirement here. -numpy = ">=1.24" +numpy = [ + { version = ">=1.24", python = "3.8" }, + { version = ">=1.25", python = "^3.9" } +] pydantic = "^2.5" lxml = ">=4.6" meshkernel = "^4.2.0" From d1e8e740560d15e1c9cf9a943d65a6941e606c3a Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Thu, 10 Oct 2024 16:10:29 +0200 Subject: [PATCH 19/48] update poetry lock --- poetry.lock | 925 ++++++++++++++++++++++++++++++---------------------- 1 file changed, 532 insertions(+), 393 deletions(-) diff --git a/poetry.lock b/poetry.lock index c68a9f24c..f045c95fa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,15 +11,18 @@ files = [ {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + [[package]] name = "anyio" -version = "4.6.0" +version = "4.5.0" description = "High level compatibility layer for multiple 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Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 10:12:04 +0200 Subject: [PATCH 21/48] updated poetry action --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 359d0b854..1aec5df72 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,11 +7,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.8", "3.9", "3.11", "3.12"] os: [ubuntu-latest, windows-latest, macos-13] runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: fetch-depth: 0 @@ -21,9 +21,9 @@ jobs: python-version: ${{ matrix.python-version }} - name: Run image - uses: abatilo/actions-poetry@v2 + uses: abatilo/actions-poetry@v3 with: - poetry-version: 1.8.2 + poetry-version: 1.8.3 - name: Cache Poetry virtualenv uses: actions/cache@v3 id: cache From 9dc7ae3366d41583fb58ab626170960eaa044448 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 10:17:05 +0200 Subject: [PATCH 22/48] updated ci to avoid deprecation warnings node.js --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1aec5df72..940c901b5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,7 @@ jobs: fetch-depth: 0 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} From 428d747fca631dd9f7de6f620a62c279d55d8151 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 10:18:12 +0200 Subject: [PATCH 23/48] updated ci to avoid deprecation warnings node.js --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 940c901b5..4391fb9f0 100644 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"^3.8" }, + { version = ">=1.2.1", python = "^3.12" } +] mkdocs-table-reader-plugin = "^0.6.1" openpyxl = "^3.0.9" mike = "^1.1.2" @@ -55,11 +63,15 @@ markupsafe = "<2.1" mkdocs-jupyter = "^0.21.0" jupyter = "^1.0.0" ipykernel = "^6.15.0" -xarray = ">=2023.0.0" +# specify to avoid poetry installation of xarray 2023.1.0 on python 3.12 (which does not support numpy 2.0) +xarray = [ + { version = ">=2023.0.0", python = "^3.8" }, + { version = ">=2024.6.0", python = "^3.12" } +] # pandas dependency comes from xarray, specify to avoid poetry installation of pandas 2.0.3 on python 3.12 pandas = [ { version = ">=1.3", python = "^3.8" }, - { version = "^2.2.0", python = "3.12" } + { version = "^2.2.0", python = "^3.12" } ] [tool.commitizen] From 81c600613aa29b22408f632866e8512592dc4879 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 11:22:14 +0200 Subject: [PATCH 27/48] numpy 2 support --- pyproject.toml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f4fee6f2c..eeb15937d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,13 +47,13 @@ mypy = "^0.910" devtools = "^0.6.1" # specify to avoid poetry installation of matplotlib 3.7.5 on python 3.12 (which does not support numpy 2.0) matplotlib = [ - { version = "^3.4", python = "^3.8" }, - { version = "^3.8", python = "^3.12" } + { version = "^3.4", python = "3.8" }, + { version = "^3.8", python = "^3.9" } ] # contourpy dependency comes from matplotlib, specify to avoid poetry installation of contourpy 1.1.1 on python 3.12 (which does not support numpy 2.0) contourpy = [ - { version = ">=1.0.1", python = "^3.8" }, - { version = ">=1.2.1", python = "^3.12" } + { version = ">=1.0.1", python = "3.8" }, + { version = ">=1.2.1", python = "^3.9" } ] mkdocs-table-reader-plugin = "^0.6.1" openpyxl = "^3.0.9" @@ -65,13 +65,13 @@ jupyter = "^1.0.0" ipykernel = "^6.15.0" # specify to avoid poetry installation of xarray 2023.1.0 on python 3.12 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1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4391fb9f0..aab90835a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -40,6 +40,10 @@ jobs: run: poetry install if: steps.cache.outputs.cache-hit != 'true' + - name: list env contents + run: | + pip list + - name: Test with pytest run: poetry run pytest --cov . --cov-report xml:coverage-reports/coverage-hydrolib-core.xml --junitxml=xunit-reports/xunit-result-hydrolib-core.xml From d2e6b8bfb99ecfe0121ce19cc92a85e4e8ba3e46 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 11:33:24 +0200 Subject: [PATCH 30/48] list env contents --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index aab90835a..d6b73858c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,6 +42,7 @@ jobs: - name: list env contents run: | + conda list pip list - name: Test with pytest From da47f5fbf8de13dcba291f0bb55cd7ced98c9ab0 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 11:35:57 +0200 Subject: [PATCH 31/48] list env contents --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d6b73858c..78cca4199 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,7 +42,7 @@ jobs: - name: list env contents run: | - conda list + poetry show pip list - name: Test with pytest From b113fa174792d255c41b307248f53abe8be2a210 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 11:45:43 +0200 Subject: [PATCH 32/48] remove snake from poetry.lock to facilitate poetry show on github --- .github/workflows/ci.yml | 2 +- poetry.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 78cca4199..ce1404de5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,7 +49,7 @@ jobs: run: poetry run pytest --cov . --cov-report xml:coverage-reports/coverage-hydrolib-core.xml --junitxml=xunit-reports/xunit-result-hydrolib-core.xml - name: Autoformat code if the check fails - if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.8) }} + if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.12) }} run: | poetry run isort . poetry run black . diff --git a/poetry.lock b/poetry.lock index a496f0dec..22bf00795 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2290,7 +2290,7 @@ files = [ [[package]] name = "mergedeep" version = "1.3.4" -description = "A deep merge function for 🐍." +description = "A deep merge function for." optional = false python-versions = ">=3.6" files = [ From 15ad030636332f0c5811b0a69c186cae15401f60 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 12:03:31 +0200 Subject: [PATCH 33/48] omit poetry config --- .github/workflows/ci.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ce1404de5..34d3ce413 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,11 +31,6 @@ jobs: path: ~/.virtualenvs key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }} - - name: Set Poetry config - run: | - poetry config virtualenvs.in-project false - poetry config virtualenvs.path ~/.virtualenvs - - name: Install Dependencies run: poetry install if: steps.cache.outputs.cache-hit != 'true' From dc01edb0b92c882c49d6a0b555d3892c0827969e Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 12:06:58 +0200 Subject: [PATCH 34/48] revert github actions poetry v2 to see if warnings dissolve --- .github/workflows/ci.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 34d3ce413..c174cc69a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,7 +21,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Run image - uses: abatilo/actions-poetry@v3 + uses: abatilo/actions-poetry@v2 with: poetry-version: 1.8.3 - name: Cache Poetry virtualenv @@ -31,6 +31,11 @@ jobs: path: ~/.virtualenvs key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }} + - name: Set Poetry config + run: | + poetry config virtualenvs.in-project false + poetry config virtualenvs.path ~/.virtualenvs + - name: Install Dependencies run: poetry install if: steps.cache.outputs.cache-hit != 'true' From 0c9616b342518dae4d1cd2c4a2f124a80ef8b33c Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 12:16:59 +0200 Subject: [PATCH 35/48] netcdf4_classic instead --- hydrolib/core/dflowfm/net/writer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hydrolib/core/dflowfm/net/writer.py b/hydrolib/core/dflowfm/net/writer.py index 595b8fb1a..cb838a807 100644 --- a/hydrolib/core/dflowfm/net/writer.py +++ b/hydrolib/core/dflowfm/net/writer.py @@ -90,7 +90,7 @@ def _create_netcdf( self, path: Path, dfm_version: str, dimr_version: str, suite_version: str ) -> nc.Dataset: # type: ignore[import] - file_format = "NETCDF3_CLASSIC" # "NETCDF4" + file_format = "NETCDF4_CLASSIC" # "NETCDF4" ncfile = nc.Dataset(path, "w", format=file_format) # type: ignore[import] UgridWriter._set_global_attributes(ncfile, path) From 51aa6f5054dc91a98b6ba549e7f5a1b330aa1593 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 12:24:16 +0200 Subject: [PATCH 36/48] netcdf4_classic instead --- hydrolib/core/dflowfm/net/reader.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/hydrolib/core/dflowfm/net/reader.py b/hydrolib/core/dflowfm/net/reader.py index 9d010f1da..d12476623 100644 --- a/hydrolib/core/dflowfm/net/reader.py +++ b/hydrolib/core/dflowfm/net/reader.py @@ -53,7 +53,7 @@ def read_mesh1d_network1d(self, mesh1d: Mesh1d) -> None: return # If the mesh is not given (default), use the networks one - ds = nc.Dataset(self._ncfile_path) # type: ignore[import] + ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] # Read mesh1d for meshkey, nckey in self._explorer.mesh1d_var_name_mapping.items(): @@ -83,7 +83,7 @@ def read_mesh2d(self, mesh2d: Mesh2d) -> None: logging.debug("Mesh2d is not found in the dataset, reading is skipped.") return - ds = nc.Dataset(self._ncfile_path) # type: ignore[import] + ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] mapping = self._explorer.mesh2d_var_name_mapping @@ -118,7 +118,7 @@ def read_link1d2d(self, link1d2d: Link1d2d) -> None: logging.debug("Link1d2d is not found in the dataset, reading is skipped.") return - ds = nc.Dataset(self._ncfile_path) # type: ignore[import] + ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] # Read mesh1d link1d2d_contact_type_arr = self._read_nc_attribute(ds["link1d2d_contact_type"]) @@ -202,7 +202,7 @@ def from_file_path(cls, file_path: Path) -> "NCExplorer": NCExplorer: A newly initialized NCExplorer. """ conventions = NCExplorer._read_ugrid_conventions() - dataset = nc.Dataset(file_path) # type: ignore[import] + dataset = nc.Dataset(file_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] keys = NCExplorer._determine_keys(dataset) network1d_mapping = NCExplorer._retrieve_variable_names_mapping( From c59ae1d9f8708f356be42ab009d6f793c001a486 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 12:29:52 +0200 Subject: [PATCH 37/48] revert --- hydrolib/core/dflowfm/net/reader.py | 8 ++++---- hydrolib/core/dflowfm/net/writer.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/hydrolib/core/dflowfm/net/reader.py b/hydrolib/core/dflowfm/net/reader.py index d12476623..9d010f1da 100644 --- a/hydrolib/core/dflowfm/net/reader.py +++ b/hydrolib/core/dflowfm/net/reader.py @@ -53,7 +53,7 @@ def read_mesh1d_network1d(self, mesh1d: Mesh1d) -> None: return # If the mesh is not given (default), use the networks one - ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] + ds = nc.Dataset(self._ncfile_path) # type: ignore[import] # Read mesh1d for meshkey, nckey in self._explorer.mesh1d_var_name_mapping.items(): @@ -83,7 +83,7 @@ def read_mesh2d(self, mesh2d: Mesh2d) -> None: logging.debug("Mesh2d is not found in the dataset, reading is skipped.") return - ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] + ds = nc.Dataset(self._ncfile_path) # type: ignore[import] mapping = self._explorer.mesh2d_var_name_mapping @@ -118,7 +118,7 @@ def read_link1d2d(self, link1d2d: Link1d2d) -> None: logging.debug("Link1d2d is not found in the dataset, reading is skipped.") return - ds = nc.Dataset(self._ncfile_path, data_model="NETCDF4_CLASSIC") # type: ignore[import] + ds = nc.Dataset(self._ncfile_path) # type: ignore[import] # Read mesh1d link1d2d_contact_type_arr = self._read_nc_attribute(ds["link1d2d_contact_type"]) @@ -202,7 +202,7 @@ def from_file_path(cls, file_path: Path) -> "NCExplorer": NCExplorer: A newly initialized NCExplorer. 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12:43:08 +0200 Subject: [PATCH 38/48] temporary higher numpy for py 3.12 --- poetry.lock | 66 ++++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 1 + 2 files changed, 65 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 22bf00795..79d309e64 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2290,7 +2290,7 @@ files = [ [[package]] name = "mergedeep" version = "1.3.4" -description = "A deep merge function for." +description = "A deep merge function for 🐍." optional = false python-versions = ">=3.6" files = [ @@ -2882,6 +2882,68 @@ files = [ {file = "numpy-2.0.2.tar.gz", hash = "sha256:883c987dee1880e2a864ab0dc9892292582510604156762362d9326444636e78"}, ] +[[package]] +name = "numpy" +version = "2.1.2" +description = "Fundamental package for array computing in Python" +optional = false +python-versions = ">=3.10" +files = [ + {file = "numpy-2.1.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = 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b/pyproject.toml index eeb15937d..b80cfa480 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ xarray = [ { version = ">=2023.0.0", python = "3.8" }, { version = ">=2024.6.0", python = "^3.9" } ] -# pandas dependency comes from xarray, specify to avoid poetry installation of pandas 2.0.3 on python 3.12 +# pandas dependency comes from xarray, specify to avoid poetry installation of pandas 2.0.3 on python 3.12 (which does not support numpy 2.0) pandas = [ { version = ">=1.3", python = "3.8" }, { version = "^2.2.0", python = "^3.9" } From 44ab76eb39bd4ef13d2f43c86dc8bfd7e9194f6c Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:01:19 +0200 Subject: [PATCH 42/48] released pytest restriction to avoid warnings --- poetry.lock | 41 +++++++++-------------------------------- pyproject.toml | 2 +- 2 files changed, 10 insertions(+), 33 deletions(-) diff --git a/poetry.lock b/poetry.lock index a496f0dec..b6dad5af7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -185,16 +185,6 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} -[[package]] -name = "atomicwrites" -version = "1.4.1" -description = "Atomic file writes." -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -files = [ - {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, -] - [[package]] name = "attrs" version = "24.2.0" @@ -3350,17 +3340,6 @@ files = [ [package.extras] tests = ["pytest"] -[[package]] -name = "py" -version = "1.11.0" -description = "library with cross-python path, ini-parsing, io, code, log facilities" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -files = [ - {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"}, - {file = "py-1.11.0.tar.gz", hash = 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+31,7 @@ meshkernel = "^4.2.0" strenum = "^0" [tool.poetry.dev-dependencies] -pytest = "^6.2" +pytest = ">=6.2" black = "^24.3" isort = "^5.8" mkdocs = "^1.2" From e5996f61008745eefbc2cc43f9b57c97bd99bfc3 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:05:59 +0200 Subject: [PATCH 43/48] released pytest restriction to avoid warnings --- poetry.lock | 18 ++++++++++-------- pyproject.toml | 2 +- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/poetry.lock b/poetry.lock index b6dad5af7..e1055c82e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -768,6 +768,9 @@ files = [ {file = "coverage-7.6.1.tar.gz", hash = "sha256:953510dfb7b12ab69d20135a0662397f077c59b1e6379a768e97c59d852ee51d"}, ] +[package.dependencies] +tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} + [package.extras] toml = ["tomli"] @@ -3564,22 +3567,21 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", 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+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] [[package]] name = "python-dateutil" @@ -4575,4 +4577,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "b1cf34ac0e9350749e041fdd90b3f6fda9ac04aeb8c755d03dcdf9215df2682b" +content-hash = "de22379d0e7b27cc166ac63ef67c240a4b8f314ff48755160bc5d368232c60bf" diff --git a/pyproject.toml b/pyproject.toml index 3253b9a99..b28d7c43f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ strenum = "^0" [tool.poetry.dev-dependencies] pytest = ">=6.2" +pytest-cov = ">=2.11" black = "^24.3" isort = "^5.8" mkdocs = "^1.2" @@ -39,7 +40,6 @@ mkdocs-material = "^8.0" mkdocstrings = "^0.16" mkdocs-autorefs = "^0.3, !=0.3.1" mkdocs-macros-plugin = "^0.6.3" -pytest-cov = "^2.11" pymdown-extensions = "^9.1" commitizen = "^2.17" flake8 = "^3.9.2" From 360d890d181e366054524f39e2e64357279ba768 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:11:22 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python 3.12 (which does not support numpy 2.0) matplotlib = [ { version = "^3.4", python = "3.8" }, @@ -55,14 +45,6 @@ contourpy = [ { version = ">=1.0.1", python = "3.8" }, { version = ">=1.2.1", python = "^3.9" } ] -mkdocs-table-reader-plugin = "^0.6.1" -openpyxl = "^3.0.9" -mike = "^1.1.2" -jinja2 = "<4" -markupsafe = "<2.1" -mkdocs-jupyter = "^0.21.0" -jupyter = "^1.0.0" -ipykernel = "^6.15.0" # specify to avoid poetry installation of xarray 2023.1.0 on python 3.12 (which does not support numpy 2.0) xarray = [ { version = ">=2023.0.0", python = "3.8" }, From e4269aee725fc7da8ab60f49d03e2995074a36c4 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:16:35 +0200 Subject: [PATCH 45/48] temporarily removed deps --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 8355651ff..ea053aa52 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,6 +35,7 @@ pytest = ">=6.2" pytest-cov = ">=2.11" black = ">=24.3" isort = ">=5.8" +devtools = ">=0.6.1" # specify to avoid poetry installation of matplotlib 3.7.5 on python 3.12 (which does not support numpy 2.0) matplotlib = [ { version = "^3.4", python = "3.8" }, From b2449b4421c848bcdc312b3b0b4446246f70f761 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:17:28 +0200 Subject: [PATCH 46/48] temporarily removed deps --- poetry.lock | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 63 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 0a6714337..c278683d9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,6 +14,24 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} +[[package]] +name = "asttokens" +version = "2.4.1" +description = "Annotate AST trees with source code positions" +optional = false +python-versions = "*" +files = [ + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = 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+[package.dependencies] +asttokens = ">=2.0.0,<3.0.0" +executing = ">=1.1.1" +pygments = ">=2.15.0" + [[package]] name = "exceptiongroup" version = "1.2.2" @@ -412,6 +446,20 @@ files = [ [package.extras] test = ["pytest (>=6)"] +[[package]] +name = "executing" +version = "2.1.0" +description = "Get the currently executing AST node of a frame, and other information" +optional = false +python-versions = ">=3.8" +files = [ + {file = "executing-2.1.0-py2.py3-none-any.whl", hash = "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf"}, + {file = "executing-2.1.0.tar.gz", hash = "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"}, +] + +[package.extras] +tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"] + [[package]] name = "fonttools" version = "4.54.1" @@ -1574,6 +1622,20 @@ files = [ [package.dependencies] typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0" +[[package]] +name = "pygments" +version = "2.18.0" +description = "Pygments is a syntax highlighting package written in Python." +optional = false +python-versions = ">=3.8" +files = [ + {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"}, + {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"}, +] + +[package.extras] +windows-terminal = ["colorama (>=0.4.6)"] + [[package]] name = "pyparsing" version = "3.1.4" @@ -1783,4 +1845,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "f8616468b8537b6329625ccdfb9a1638f6715957fef5c45859424ba18b7a8aff" +content-hash = "36f5096b718e05f24d604f75ba1812eb2c0362aaf652e25ac92773685b9f1000" From 469d18991eacfab66256fcd52c27704bf6db81d6 Mon Sep 17 00:00:00 2001 From: veenstrajelmer Date: Fri, 11 Oct 2024 13:20:22 +0200 Subject: [PATCH 47/48] reverted --- poetry.lock | 2950 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