From 90d58f9bd5bba2edf6a5a2813a40439dcc8a614a Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 13:26:58 +0100 Subject: [PATCH 01/38] Update install.sh --- scripts/install.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install.sh b/scripts/install.sh index f4cf1f5..95a2fd3 100644 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -14,6 +14,7 @@ install_test_requirements_only () { install_requirements() { python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin + python3 -m pip install --upgrade pip==23.0.1 } From 6ffe26ab4e3cce7e74681fc4e7658f5b304432f3 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 14:09:27 +0100 Subject: [PATCH 02/38] Update ci_petsc.yml --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 198367e..77b468f 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -56,7 +56,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: [3.7, 3.8, 3.9, "3.10", 3.11] + python-version: [3.7, 3.8, 3.9, 3.10, 3.11] mpi: ["openmpi"] steps: From 82de6cf93b075f9b39545697f83254d152af27fe Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 14:37:49 +0100 Subject: [PATCH 03/38] Remove Python v3.10 Test seemed to fail for v3.10 but might pass for others. Want to see if petsc and petsc4py successful compile now that pip is pinned to 23.0.1. --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 77b468f..d8b92bb 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -56,7 +56,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: [3.7, 3.8, 3.9, 3.10, 3.11] + python-version: [3.7, 3.8, 3.9, 3.11] mpi: ["openmpi"] steps: From 28a0cb31ce64b33f403ffea3b63ac8b41943bdd6 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 15:17:20 +0100 Subject: [PATCH 04/38] Enable ```--use-pep517``` for petsc install Suggestion from warning message: ```DEPRECATION: petsc4py is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/8559``` --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index d8b92bb..db8afe6 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -88,7 +88,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.18.4" "petsc4py==3.18.4" + run: pip install --use-pep517 "petsc==3.18.4" "petsc4py==3.18.4" env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From eaa253f8c0d7773c0f4b59b61a353023711b3b05 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 15:18:41 +0100 Subject: [PATCH 05/38] Add back python v3.10 Lets see if this one still fails to build petsc! --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index db8afe6..f45750d 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -56,7 +56,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: [3.7, 3.8, 3.9, 3.11] + python-version: [3.7, 3.8, 3.9, "3.10", 3.11] mpi: ["openmpi"] steps: From 98ea6c229e29b7431b4b97473086174ce57db9e9 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 15:43:05 +0100 Subject: [PATCH 06/38] Tag meant to be `--no-use-pep517` --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index f45750d..0e49eb5 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -88,7 +88,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install --use-pep517 "petsc==3.18.4" "petsc4py==3.18.4" + run: pip install --no-use-pep517 "petsc==3.18.4" "petsc4py==3.18.4" env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From f8ba23e60d49abec6e62b514b848fee357da449a Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Thu, 4 May 2023 17:16:48 +0100 Subject: [PATCH 07/38] Update `petsc` and `petsc4py` to version `3.19.1`. --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 0e49eb5..55b1a0d 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -88,7 +88,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install --no-use-pep517 "petsc==3.18.4" "petsc4py==3.18.4" + run: pip install --no-use-pep517 "petsc==3.19.1" "petsc4py==3.19.1" env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From ea2f7dd330404ca322272f5fc2107c5c6697625e Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 11:26:10 +0100 Subject: [PATCH 08/38] `fail-fast: false` to allow different Python version to complete --- .github/workflows/ci_petsc.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 55b1a0d..b715903 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -54,6 +54,7 @@ jobs: tests: runs-on: ${{ matrix.os }} strategy: + fail-fast: false matrix: os: [ubuntu-latest] python-version: [3.7, 3.8, 3.9, "3.10", 3.11] From 85ceb14fbaa6df23e0cd93d5825845403113863e Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 13:49:43 +0100 Subject: [PATCH 09/38] Update install.sh --- scripts/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install.sh b/scripts/install.sh index 95a2fd3..42f6864 100644 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -14,7 +14,7 @@ install_test_requirements_only () { install_requirements() { python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin - python3 -m pip install --upgrade pip==23.0.1 + python3 -m pip install --upgrade pip==23.0.1 setuptools wheel } From 1b154ef20bbe5eee72a737c0a4de19b49a138c07 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 13:50:05 +0100 Subject: [PATCH 10/38] Update ci_petsc.yml --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index b715903..9ff907b 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install --no-use-pep517 "petsc==3.19.1" "petsc4py==3.19.1" + run: pip install "petsc==3.19.1" "petsc4py==3.19.1" env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From d9693b78545c23bbccfeafa549fe0c0c64f5516f Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 15:33:01 +0100 Subject: [PATCH 11/38] Use tag `--no-binary :all:` for `pip==23.0.1` anchoring --- scripts/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install.sh b/scripts/install.sh index 42f6864..52ac0d8 100644 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -14,7 +14,7 @@ install_test_requirements_only () { install_requirements() { python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin - python3 -m pip install --upgrade pip==23.0.1 setuptools wheel + python3 -m pip install --upgrade pip==23.0.1 --no-binary :all: } From 9c8945d04dd1def2e8ad7c8b5cbcaeb3aa19232b Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 17:20:18 +0100 Subject: [PATCH 12/38] Require Cython for building source C files --- scripts/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install.sh b/scripts/install.sh index 52ac0d8..73cdc42 100644 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -14,7 +14,7 @@ install_test_requirements_only () { install_requirements() { python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin - python3 -m pip install --upgrade pip==23.0.1 --no-binary :all: + python3 -m pip install --upgrade cython pip==23.0.1 --no-binary :all: } From 899dfd6dbdcfc2b809d5f6333c36aae278a4b7eb Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 18:50:22 +0100 Subject: [PATCH 13/38] Update install.sh --- scripts/install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install.sh b/scripts/install.sh index 73cdc42..95a2fd3 100644 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -14,7 +14,7 @@ install_test_requirements_only () { install_requirements() { python3 -c 'import toml; c = toml.load("pyproject.toml"); print("\n".join(c["project"]["dependencies"]))' | pip install -r /dev/stdin - python3 -m pip install --upgrade cython pip==23.0.1 --no-binary :all: + python3 -m pip install --upgrade pip==23.0.1 } From e08893f79610ebdae7a51495720ed76d147b8721 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 18:55:16 +0100 Subject: [PATCH 14/38] =?UTF-8?q?Added=20`=E2=80=94no-cache-dir`=20and=20`?= =?UTF-8?q?=E2=80=94no-binary`=20tags?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .github/workflows/ci_petsc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 9ff907b..307d029 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1" + run: pip install "petsc==3.19.1" "petsc4py==3.19.1"/ --no-cache-dir --no-binary=petsc --no-binary=petsc4py env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" @@ -102,6 +102,6 @@ jobs: - name: Upload code coverage uses: codecov/codecov-action@v2 timeout-minutes: 10 - with: + with:i token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: false From fabbb9b1307653e5556375a0e07c200e78842a4b Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 18:58:05 +0100 Subject: [PATCH 15/38] Update ci_petsc.yml --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 307d029..24e414c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1"/ --no-cache-dir --no-binary=petsc --no-binary=petsc4py + run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary=petsc --no-binary=petsc4py env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From cc47cbc73023b5569b51f9ed83185a149ae38586 Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 19:00:29 +0100 Subject: [PATCH 16/38] Missplaced `i` removed --- .github/workflows/ci_petsc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 24e414c..3f00671 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary=petsc --no-binary=petsc4py + run: pip install "petsc==3.19.1" "petsc4py==3.19.1"/ --no-cache-dir --no-binary=petsc --no-binary=petsc4py env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" @@ -102,6 +102,6 @@ jobs: - name: Upload code coverage uses: codecov/codecov-action@v2 timeout-minutes: 10 - with:i + with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: false From 7b1a8b3fbffb8739577ae50fce3e955d0939a8bf Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 19:50:30 +0100 Subject: [PATCH 17/38] Woops. Mis-typed `/` too --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 3f00671..d6bd6de 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1"/ --no-cache-dir --no-binary=petsc --no-binary=petsc4py + run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary :all: env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From cfbb53de8ef3ace7d99e11e8b0d7ca723f45462b Mon Sep 17 00:00:00 2001 From: Bradley Martin Date: Fri, 5 May 2023 19:53:13 +0100 Subject: [PATCH 18/38] Doesn't like `:all:` so replaced with more verbose code --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index d6bd6de..e3d4f52 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -89,7 +89,7 @@ jobs: run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary :all: + run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary=petsc --no-binary=petsc4py env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From d9408ac870da89bd996eac85278f653e32fc8724 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Mon, 8 May 2023 22:34:27 -0400 Subject: [PATCH 19/38] focus on py3.10 only, remove serial tests --- .github/workflows/ci_petsc.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index e3d4f52..70aefcd 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -57,7 +57,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [3.7, 3.8, 3.9, "3.10", 3.11] + python-version: ["3.10"] mpi: ["openmpi"] steps: @@ -74,9 +74,6 @@ jobs: bash scripts/install.sh bash scripts/install.sh test - - name: Run serial tests - run: pytest -v --cov --cov-report xml --cov-append ggce/_tests/*.py - - name: Setup MPI uses: mpi4py/setup-mpi@v1 with: From b5e7b0b8fd425508634efeaa20939321b73de781 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Mon, 8 May 2023 22:49:46 -0400 Subject: [PATCH 20/38] only petsc, verbose pip --- .github/workflows/ci_petsc.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 70aefcd..305ff03 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -82,11 +82,8 @@ jobs: - name: Install mpi4py and pytest-mpi run: pip install mpi4py pytest-mpi - - name: Run MPI tests - run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py - - name: Setup PETSc - run: pip install "petsc==3.19.1" "petsc4py==3.19.1" --no-cache-dir --no-binary=petsc --no-binary=petsc4py + run: pip install petsc --no-cache-dir --no-binary=petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 6363af2f43373be4dd835e8a07cb0e8c921a5943 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Mon, 8 May 2023 22:54:01 -0400 Subject: [PATCH 21/38] try with --no-use-pep517 --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 305ff03..facf42c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -83,7 +83,7 @@ jobs: run: pip install mpi4py pytest-mpi - name: Setup PETSc - run: pip install petsc --no-cache-dir --no-binary=petsc --verbose + run: pip install petsc --no-cache-dir --no-use-pep517 --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 71c3d38b94951435b60271fcca888ef716766ea7 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Mon, 8 May 2023 22:58:52 -0400 Subject: [PATCH 22/38] use pep517 --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index facf42c..e1acc7a 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -83,7 +83,7 @@ jobs: run: pip install mpi4py pytest-mpi - name: Setup PETSc - run: pip install petsc --no-cache-dir --no-use-pep517 --verbose + run: pip install petsc --no-cache-dir --use-pep517 --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 9d7ade48f17917e81064a6e9c752448e05113c79 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Mon, 8 May 2023 23:03:42 -0400 Subject: [PATCH 23/38] new flags --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index e1acc7a..ed1dc4d 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -83,7 +83,7 @@ jobs: run: pip install mpi4py pytest-mpi - name: Setup PETSc - run: pip install petsc --no-cache-dir --use-pep517 --verbose + run: pip install petsc --no-cache-dir --no-binary --only-binary --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 4cf43cdf469d462bb90faeda2455998481756c33 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Tue, 9 May 2023 09:17:54 -0400 Subject: [PATCH 24/38] install wheel by hand --- .github/workflows/ci_petsc.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index ed1dc4d..7faa8a2 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -83,7 +83,8 @@ jobs: run: pip install mpi4py pytest-mpi - name: Setup PETSc - run: pip install petsc --no-cache-dir --no-binary --only-binary --verbose + run: pip install wheel + run: pip install petsc --no-cache-dir --no-use-pep517 --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 3490797dbd73faf7ad4a817ccacdaf05fbe9c581 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Tue, 9 May 2023 09:23:25 -0400 Subject: [PATCH 25/38] typo in install --- .github/workflows/ci_petsc.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 7faa8a2..ebf05be 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -82,8 +82,10 @@ jobs: - name: Install mpi4py and pytest-mpi run: pip install mpi4py pytest-mpi - - name: Setup PETSc + - name: Install wheel run: pip install wheel + + - name: Setup PETSc run: pip install petsc --no-cache-dir --no-use-pep517 --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 7cdef3e99323aa84c07cdfb09f8277f05d2953b9 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Tue, 9 May 2023 09:28:30 -0400 Subject: [PATCH 26/38] install setuptools manually --- .github/workflows/ci_petsc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index ebf05be..c32735c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -82,8 +82,8 @@ jobs: - name: Install mpi4py and pytest-mpi run: pip install mpi4py pytest-mpi - - name: Install wheel - run: pip install wheel + - name: Install wheel and setuptools manually + run: pip install wheel setuptools - name: Setup PETSc run: pip install petsc --no-cache-dir --no-use-pep517 --verbose From a71fba3b95e12db02a0b2ba935cc4a72053163e5 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 12:10:24 -0400 Subject: [PATCH 27/38] force github actions to continue on pip error --- .github/workflows/ci_petsc.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index c32735c..8643ffc 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -86,6 +86,7 @@ jobs: run: pip install wheel setuptools - name: Setup PETSc + continue-on-error: true run: pip install petsc --no-cache-dir --no-use-pep517 --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 16f0e196ac6a6f181557ad2ed005e433539208d5 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 12:23:18 -0400 Subject: [PATCH 28/38] check standard error message --- .github/workflows/ci_petsc.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 8643ffc..0704e7a 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -86,8 +86,7 @@ jobs: run: pip install wheel setuptools - name: Setup PETSc - continue-on-error: true - run: pip install petsc --no-cache-dir --no-use-pep517 --verbose + run: pip install petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" From 67b461e312ef6654d1734c515630f1c91136d703 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 12:33:59 -0400 Subject: [PATCH 29/38] check pip versions used in diff py versions --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 0704e7a..c224de6 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -57,7 +57,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: ["3.10"] + python-version: ["3.9", "3.10"] mpi: ["openmpi"] steps: From 84a44985bb333deb057975feb42689dc90774093 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 13:14:30 -0400 Subject: [PATCH 30/38] downgrading pip --- .github/workflows/ci_petsc.yml | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index c224de6..2f5b70d 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -57,7 +57,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: ["3.9", "3.10"] + python-version: ["3.10"] mpi: ["openmpi"] steps: @@ -85,20 +85,10 @@ jobs: - name: Install wheel and setuptools manually run: pip install wheel setuptools + - name: Downgrade pip + run: pip install pip==23.0.1 + - name: Setup PETSc run: pip install petsc --verbose env: - PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" - - - name: Run PETSc tests - run: mpiexec -n 4 coverage run --rcfile=ggce/_tests/petsc/setup_pytest_petsc_mpi.cfg -m pytest -v --with-mpi ggce/_tests/petsc/*.py - - - name: Combine coverage reports from all ranks and generate xml report - run: coverage combine && coverage xml - - - name: Upload code coverage - uses: codecov/codecov-action@v2 - timeout-minutes: 10 - with: - token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: false + PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From daae7734c916aaf4fe9576d18a08fd67318140bb Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 14:46:01 -0400 Subject: [PATCH 31/38] try with cont on error --- .github/workflows/ci_petsc.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 2f5b70d..1af1d4b 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -90,5 +90,6 @@ jobs: - name: Setup PETSc run: pip install petsc --verbose + continue-on-error: true env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From 059f57b41879dd0301d582bdb71e320c51050688 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 15:27:37 -0400 Subject: [PATCH 32/38] check if pip downgrade works --- .github/workflows/ci.yml | 20 ++++++++++---------- .github/workflows/ci_petsc.yml | 3 +++ 2 files changed, 13 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 72cd8dc..0eb3236 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -120,19 +120,19 @@ jobs: bash scripts/install.sh bash scripts/install.sh test - - name: Run serial tests - run: pytest -v --cov --cov-report xml --cov-append ggce/_tests/*.py + # - name: Run serial tests + # run: pytest -v --cov --cov-report xml --cov-append ggce/_tests/*.py - - name: Setup MPI - uses: mpi4py/setup-mpi@v1 - with: - mpi: ${{ matrix.mpi }} + # - name: Setup MPI + # uses: mpi4py/setup-mpi@v1 + # with: + # mpi: ${{ matrix.mpi }} - - name: Install mpi4py and pytest-mpi - run: pip install mpi4py pytest-mpi + # - name: Install mpi4py and pytest-mpi + # run: pip install mpi4py pytest-mpi - - name: Run MPI tests - run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py + # - name: Run MPI tests + # run: mpiexec -n 2 coverage run --rcfile=ggce/_tests/mpi/setup_pytest_mpi.cfg -m pytest -v --with-mpi ggce/_tests/mpi/*.py # - name: Combine coverage reports from all ranks and generate xml report # run: coverage combine && coverage xml diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 1af1d4b..d499282 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -88,6 +88,9 @@ jobs: - name: Downgrade pip run: pip install pip==23.0.1 + - name: Check version of pip + run: pip -V + - name: Setup PETSc run: pip install petsc --verbose continue-on-error: true From 023133916dbd64b6524a7b0fbe268fb30209314d Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 15:34:29 -0400 Subject: [PATCH 33/38] force pip downgrade --- .github/workflows/ci_petsc.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index d499282..9e0788f 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -82,17 +82,16 @@ jobs: - name: Install mpi4py and pytest-mpi run: pip install mpi4py pytest-mpi - - name: Install wheel and setuptools manually - run: pip install wheel setuptools - - name: Downgrade pip - run: pip install pip==23.0.1 + run: pip install pip==23.0.1 --verbose - name: Check version of pip run: pip -V - name: Setup PETSc - run: pip install petsc --verbose - continue-on-error: true + run: | + pip install pip=23.0.1 --verbose + pip -V + pip install petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From b019133ca044d110e33edcd8dd6651cbdd2725c1 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 15:39:36 -0400 Subject: [PATCH 34/38] fixed typo = to == --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 9e0788f..1c6b28c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -90,7 +90,7 @@ jobs: - name: Setup PETSc run: | - pip install pip=23.0.1 --verbose + pip install pip==23.0.1 --verbose pip -V pip install petsc --verbose env: From e760edc6a01ed0334a6b1f2c87e86ea1397b06d9 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 15:55:10 -0400 Subject: [PATCH 35/38] check pip version earlier --- .github/workflows/ci_petsc.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 1c6b28c..eca858d 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -71,6 +71,7 @@ jobs: - name: Install requirements run: | + pip -V bash scripts/install.sh bash scripts/install.sh test @@ -85,13 +86,11 @@ jobs: - name: Downgrade pip run: pip install pip==23.0.1 --verbose - - name: Check version of pip - run: pip -V + - name: Check version of pip with direct reference to location + run: /opt/hostedtoolcache/Python/3.10.11/bin/pip -V - name: Setup PETSc run: | - pip install pip==23.0.1 --verbose - pip -V - pip install petsc --verbose + /opt/hostedtoolcache/Python/3.10.11/bin/pip install petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From c0ddd7cdb648e84f485525223288be54e9286d28 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 16:09:25 -0400 Subject: [PATCH 36/38] uninstall and reinstall pip using ensurepip module --- .github/workflows/ci_petsc.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index eca858d..a02008b 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -84,13 +84,14 @@ jobs: run: pip install mpi4py pytest-mpi - name: Downgrade pip - run: pip install pip==23.0.1 --verbose - - - name: Check version of pip with direct reference to location - run: /opt/hostedtoolcache/Python/3.10.11/bin/pip -V + run: | + pip uninstall pip + python -m ensurepip + pip -V - name: Setup PETSc run: | - /opt/hostedtoolcache/Python/3.10.11/bin/pip install petsc --verbose + pip -V + pip install petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From 152872335c3f8bae82e1c0f6d11663fcd18ecf1c Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 16:12:41 -0400 Subject: [PATCH 37/38] fix typo --- .github/workflows/ci_petsc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index a02008b..3bdbf0c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -91,7 +91,7 @@ jobs: - name: Setup PETSc run: | - pip -V + pip -V pip install petsc --verbose env: PETSC_CONFIGURE_OPTIONS: "--with-scalar-type=complex --download-mumps --download-scalapack" \ No newline at end of file From 8a33660d6f10402b238a7541e6b1d4b427ff6cd6 Mon Sep 17 00:00:00 2001 From: Stepan Fomichev Date: Fri, 12 May 2023 16:19:34 -0400 Subject: [PATCH 38/38] push -y to avoid prompt with uninstall --- .github/workflows/ci_petsc.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci_petsc.yml b/.github/workflows/ci_petsc.yml index 3bdbf0c..c6f5e2c 100644 --- a/.github/workflows/ci_petsc.yml +++ b/.github/workflows/ci_petsc.yml @@ -72,6 +72,7 @@ jobs: - name: Install requirements run: | pip -V + pip3 -V bash scripts/install.sh bash scripts/install.sh test @@ -85,9 +86,12 @@ jobs: - name: Downgrade pip run: | - pip uninstall pip + pip -V + pip3 -V + pip uninstall -y pip python -m ensurepip pip -V + pip3 -V - name: Setup PETSc run: |