From aa068dbfb71e799ea0691f703b4b7cc30bb1a7b4 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Thu, 14 Dec 2023 23:00:08 +0100 Subject: [PATCH 01/26] migrate from osx-11 to osx-12 --- .github/workflows/c-cpp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index f6ffdf46b..d9404c6f1 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -71,7 +71,7 @@ jobs: strategy: matrix: # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners - os: [macos-11] + os: [macos-12] runs-on: ${{ matrix.os }} steps: - name: Install dependencies From e30b96dbc405a387e53ba953b55e34d5a7ed23d6 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 07:56:38 +0100 Subject: [PATCH 02/26] add debugging command --- .github/workflows/c-cpp.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index d9404c6f1..8de9b82aa 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -92,6 +92,15 @@ jobs: run: make -j 3 - name: make install run: sudo make install + + - name: debug + run: | + ls -latr /Users/runner/work/gapc/gapc/lib/rtlib && True; + ls /Users && True; + ls /Users/runner && True; + ls /Users/runner/work && True; + ls /Users/runner/work/gapc && True; + ls /Users/runner/work/gapc/lib && True; - name: test-mod run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx From d5a41cee632ed7d997b75f8753d3689216f78a22 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 08:05:06 +0100 Subject: [PATCH 03/26] more debug --- .github/workflows/c-cpp.yml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 8de9b82aa..afca088a1 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -93,14 +93,18 @@ jobs: - name: make install run: sudo make install - - name: debug - run: | - ls -latr /Users/runner/work/gapc/gapc/lib/rtlib && True; - ls /Users && True; - ls /Users/runner && True; - ls /Users/runner/work && True; - ls /Users/runner/work/gapc && True; - ls /Users/runner/work/gapc/lib && True; + - name: debug1 + run: ls /Users + - name: debug2 + run: ls /Users/runner && True; + - name: debug3 + run: ls /Users/runner/work && True; + - name: debug4 + run: ls /Users/runner/work/gapc && True; + - name: debug5 + run: ls /Users/runner/work/gapc/lib && True; + - name: debug6 + run: ls -latr /Users/runner/work/gapc/gapc/lib/rtlib && True; - name: test-mod run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx From 7135e030a5753b9fb6884f0ffca668d2b830e582 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 08:55:11 +0100 Subject: [PATCH 04/26] more debug --- .github/workflows/c-cpp.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index afca088a1..b7ed39ce7 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -93,6 +93,10 @@ jobs: - name: make install run: sudo make install + - name: debug0 + run: find / -name "*librna*" 2> /dev/null + - name: debug0 + run: which -a gapc - name: debug1 run: ls /Users - name: debug2 From f6635b6e2f59e24845274c2d5f55f645a3f7c589 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 10:46:51 +0100 Subject: [PATCH 05/26] fixing linker paths for runtime compilation --- config.mf.in | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config.mf.in b/config.mf.in index d71af1adc..67cf2dddc 100644 --- a/config.mf.in +++ b/config.mf.in @@ -84,8 +84,7 @@ LDLIBS = $(RTLIB_LDLIBS) \ RT_LDLIBS = $(GSL_LIBS) -lrna # set to RTLIB_LDFLAGS RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL) \ - -L$(PREFIX)$(LIB_PATH)/$(LIB_RT) \ - -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) \ + -L$(PREFIX)$(LIB_PATH) # set to RTLIB_CPPFLAGS RT_CPPFLAGS = $(GSL_CFLAGS) \ -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_GENERAL) \ From 15e1cbd3981f77c782c0a9aab11277204d3e307c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 10:47:44 +0100 Subject: [PATCH 06/26] remove debug info --- .github/workflows/c-cpp.yml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index b7ed39ce7..3b1e74a28 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -92,24 +92,6 @@ jobs: run: make -j 3 - name: make install run: sudo make install - - - name: debug0 - run: find / -name "*librna*" 2> /dev/null - - name: debug0 - run: which -a gapc - - name: debug1 - run: ls /Users - - name: debug2 - run: ls /Users/runner && True; - - name: debug3 - run: ls /Users/runner/work && True; - - name: debug4 - run: ls /Users/runner/work/gapc && True; - - name: debug5 - run: ls /Users/runner/work/gapc/lib && True; - - name: debug6 - run: ls -latr /Users/runner/work/gapc/gapc/lib/rtlib && True; - - name: test-mod run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - name: test-mod_outside From b1d7c8fe32140fda5801c8b568dbc99c7d3ce22c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 10:51:37 +0100 Subject: [PATCH 07/26] haskell/actions -> haskell-actions --- .github/workflows/c-cpp.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 3b1e74a28..50c64f9a4 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -52,7 +52,7 @@ jobs: - name: test-unit run: make test-unit # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc - - uses: haskell/actions/setup@v2 + - uses: haskell-actions/setup@v2 with: cabal-version: '3.6.2.0' # pin version on 2023-02-09 to enable proper cabal installtion id: haskell @@ -92,6 +92,7 @@ jobs: run: make -j 3 - name: make install run: sudo make install + - name: test-mod run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - name: test-mod_outside From dff1850972ebf9b74bb554f1a2522e66183a19e6 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 11:47:48 +0100 Subject: [PATCH 08/26] try to pin GHC version --- .github/workflows/c-cpp.yml | 44 ++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 50c64f9a4..b416205e5 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -75,34 +75,34 @@ jobs: runs-on: ${{ matrix.os }} steps: - name: Install dependencies - run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install + run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc@9.6 - name: update cabal run: cabal update - name: add random Haskell lib run: cabal install --lib random - - name: Checkout truth - run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + #~ - name: Checkout truth + #~ run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - - uses: actions/checkout@v3 - - name: configure - run: ./configure --prefix $GITHUB_WORKSPACE - - name: patch configuration for OSX - run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf - - name: make - run: make -j 3 - - name: make install - run: sudo make install + #~ - uses: actions/checkout@v3 + #~ - name: configure + #~ run: ./configure --prefix $GITHUB_WORKSPACE + #~ - name: patch configuration for OSX + #~ run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf + #~ - name: make + #~ run: make -j 3 + #~ - name: make install + #~ run: sudo make install - - name: test-mod - run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - - name: test-mod_outside - run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - - name: test-regress - run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - - name: test-ambiguity - run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - - name: test-unit - run: make test-unit + #~ - name: test-mod + #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx + #~ - name: test-mod_outside + #~ run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx + #~ - name: test-regress + #~ run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + #~ - name: test-ambiguity + #~ run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + #~ - name: test-unit + #~ run: make test-unit - name: test-paral run: make test-paral From f012ff8879ca0f1bf4d174ac118425c01fc45e6d Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 11:52:49 +0100 Subject: [PATCH 09/26] re-enable dependencies --- .github/workflows/c-cpp.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index b416205e5..3a0909b6a 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -80,18 +80,18 @@ jobs: run: cabal update - name: add random Haskell lib run: cabal install --lib random - #~ - name: Checkout truth - #~ run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + - name: Checkout truth + run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - #~ - uses: actions/checkout@v3 - #~ - name: configure - #~ run: ./configure --prefix $GITHUB_WORKSPACE - #~ - name: patch configuration for OSX - #~ run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf - #~ - name: make - #~ run: make -j 3 - #~ - name: make install - #~ run: sudo make install + - uses: actions/checkout@v3 + - name: configure + run: ./configure --prefix $GITHUB_WORKSPACE + - name: patch configuration for OSX + run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf + - name: make + run: make -j 3 + - name: make install + run: sudo make install #~ - name: test-mod #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx From 6d29c3a1a58ed92416457cfcd6521ff579daf417 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 12:04:20 +0100 Subject: [PATCH 10/26] downgrade GHC --- .github/workflows/c-cpp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 3a0909b6a..aa658e54d 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -75,7 +75,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - name: Install dependencies - run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc@9.6 + run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc@9.2 - name: update cabal run: cabal update - name: add random Haskell lib From fc40c3886273363f1c30fd0d28d327299c204074 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 14:31:35 +0100 Subject: [PATCH 11/26] manual ghc execution --- .github/workflows/c-cpp.yml | 122 +++++++++++++++++++----------------- 1 file changed, 65 insertions(+), 57 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index aa658e54d..f29def145 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -15,56 +15,56 @@ on: description: 'Test scenario tags' jobs: - gapc_ubuntu: - needs: cpplint - strategy: - matrix: - # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners - # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/ - # 18.04 burnout: https://github.com/actions/runner-images/issues/6002 - os: [ubuntu-20.04, ubuntu-22.04] - runs-on: ${{ matrix.os }} - steps: - - name: Update apt - run: sudo apt-get update - - name: Install dependencies - run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip + #~ gapc_ubuntu: + #~ needs: cpplint + #~ strategy: + #~ matrix: + #~ # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners + #~ # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/ + #~ # 18.04 burnout: https://github.com/actions/runner-images/issues/6002 + #~ os: [ubuntu-20.04, ubuntu-22.04] + #~ runs-on: ${{ matrix.os }} + #~ steps: + #~ - name: Update apt + #~ run: sudo apt-get update + #~ - name: Install dependencies + #~ run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip - - name: Checkout truth - run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + #~ - name: Checkout truth + #~ run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - - uses: actions/checkout@v3 - - name: configure - run: ./configure --prefix $GITHUB_WORKSPACE - - name: make - run: make -j 2 - - name: make install - run: sudo make install + #~ - uses: actions/checkout@v3 + #~ - name: configure + #~ run: ./configure --prefix $GITHUB_WORKSPACE + #~ - name: make + #~ run: make -j 2 + #~ - name: make install + #~ run: sudo make install - - name: test-mod - run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu - - name: test-mod_outside - run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu - - name: test-regress - run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - - name: test-ambiguity - run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - - name: test-unit - run: make test-unit - # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc - - uses: haskell-actions/setup@v2 - with: - cabal-version: '3.6.2.0' # pin version on 2023-02-09 to enable proper cabal installtion - id: haskell - - name: cabal - run: | - ${{ steps.haskell.outputs.cabal-exe }} v2-update - ${{ steps.haskell.outputs.cabal-exe }} v2-install --lib random + #~ - name: test-mod + #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu + #~ - name: test-mod_outside + #~ run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu + #~ - name: test-regress + #~ run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + #~ - name: test-ambiguity + #~ run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + #~ - name: test-unit + #~ run: make test-unit + #~ # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc + #~ - uses: haskell-actions/setup@v2 + #~ with: + #~ cabal-version: '3.6.2.0' # pin version on 2023-02-09 to enable proper cabal installtion + #~ id: haskell + #~ - name: cabal + #~ run: | + #~ ${{ steps.haskell.outputs.cabal-exe }} v2-update + #~ ${{ steps.haskell.outputs.cabal-exe }} v2-install --lib random - - name: test-paral - run: | - package_path=$HOME/.cabal/store/ghc-`${{ steps.haskell.outputs.ghc-exe }} --version | rev | cut -d " " -f 1 | rev`/package.db - GHC="ghc -package-db $package_path" make test-paral + #~ - name: test-paral + #~ run: | + #~ package_path=$HOME/.cabal/store/ghc-`${{ steps.haskell.outputs.ghc-exe }} --version | rev | cut -d " " -f 1 | rev`/package.db + #~ GHC="ghc -package-db $package_path" make test-paral gapc_osx: needs: cpplint @@ -75,7 +75,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - name: Install dependencies - run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc@9.2 + run: brew install bison@2.7 cmake boost gsl gnu-sed libomp gmp cabal-install ghc - name: update cabal run: cabal update - name: add random Haskell lib @@ -93,6 +93,14 @@ jobs: - name: make install run: sudo make install + - name: debug + run: which -a ghc + - name: debug1 + run: | + mkdir -p testdata/paraltest/temp + cd testdata/paraltest/temp + ghc --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain + #~ - name: test-mod #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx #~ - name: test-mod_outside @@ -107,7 +115,7 @@ jobs: run: make test-paral fold-grammars: - needs: cpplint + #~ needs: cpplint strategy: matrix: task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] @@ -142,12 +150,12 @@ jobs: perl runTests.pl 2 ${{ matrix.task }} popd - cpplint: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - - run: pip install cpplint - - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/ - - run: cpplint --counting 'detailed' --filter="-build/include_subdir,-readability/casting,-runtime/arrays" --extensions=c,h librna/rnalib.{c,h} - - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" testdata/unittest/* + #~ cpplint: + #~ runs-on: ubuntu-latest + #~ steps: + #~ - uses: actions/checkout@v3 + #~ - uses: actions/setup-python@v4 + #~ - run: pip install cpplint + #~ - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/ + #~ - run: cpplint --counting 'detailed' --filter="-build/include_subdir,-readability/casting,-runtime/arrays" --extensions=c,h librna/rnalib.{c,h} + #~ - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" testdata/unittest/* From 27dc3aa537c07e44d391e02e0395e6f07594f1a3 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 14:37:51 +0100 Subject: [PATCH 12/26] hide dependency --- .github/workflows/c-cpp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index f29def145..3cf7bce2b 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -67,7 +67,7 @@ jobs: #~ GHC="ghc -package-db $package_path" make test-paral gapc_osx: - needs: cpplint + #~ needs: cpplint strategy: matrix: # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners From 3f6f15a564713a6fc2e556832328c50e52f010bf Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 14:56:58 +0100 Subject: [PATCH 13/26] more debug --- .github/workflows/c-cpp.yml | 72 +++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 35 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 3cf7bce2b..1b4b2bc45 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -99,6 +99,8 @@ jobs: run: | mkdir -p testdata/paraltest/temp cd testdata/paraltest/temp + ghc --version + cat /Users/runner/.ghc/x86_64-darwin-9.6.2/environments/default ghc --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain #~ - name: test-mod @@ -111,44 +113,44 @@ jobs: #~ run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth #~ - name: test-unit #~ run: make test-unit - - name: test-paral - run: make test-paral + #~ - name: test-paral + #~ run: make test-paral - fold-grammars: + #~ fold-grammars: #~ needs: cpplint - strategy: - matrix: - task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] - runs-on: ubuntu-latest - steps: - # install gapcs - - name: Update apt - run: sudo apt-get update - - name: Install dependencies - run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython - - uses: actions/checkout@v3 - - name: configure - run: ./configure - - name: make - run: make -j 2 - - name: make install - run: sudo make install + #~ strategy: + #~ matrix: + #~ task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] + #~ runs-on: ubuntu-latest + #~ steps: + #~ # install gapcs + #~ - name: Update apt + #~ run: sudo apt-get update + #~ - name: Install dependencies + #~ run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython + #~ - uses: actions/checkout@v3 + #~ - name: configure + #~ run: ./configure + #~ - name: make + #~ run: make -j 2 + #~ - name: make install + #~ run: sudo make install - - name: clone fold-grammars - run: git clone --branch master https://github.com/jlab/fold-grammars.git $GITHUB_WORKSPACE/../fold-grammars - - name: configure fold-grammars - run: | - cd $GITHUB_WORKSPACE/../fold-grammars - sed -i "s#bgapDir = '/vol/gapc/'#bgapDir = '/usr/local/'#" Misc/Applications/lib/foldGrammars/Settings.pm - sed -i "s#rootDir = '/vol/fold-grammars/src/'#rootDir = '`pwd`/'#" Misc/Applications/lib/foldGrammars/Settings.pm - - name: execute tests - run: | - cd $GITHUB_WORKSPACE/../fold-grammars - if [[ "${{ matrix.task }}" == "default" ]]; then pushd .; cd Misc/Test-Suite/GeorgStyle/; bash run.sh ../Truth; cd ../StefanStyle/; python test_cofold.py; popd; fi - pushd . - cd Misc/Test-Suite/StefanStyle/ - perl runTests.pl 2 ${{ matrix.task }} - popd + #~ - name: clone fold-grammars + #~ run: git clone --branch master https://github.com/jlab/fold-grammars.git $GITHUB_WORKSPACE/../fold-grammars + #~ - name: configure fold-grammars + #~ run: | + #~ cd $GITHUB_WORKSPACE/../fold-grammars + #~ sed -i "s#bgapDir = '/vol/gapc/'#bgapDir = '/usr/local/'#" Misc/Applications/lib/foldGrammars/Settings.pm + #~ sed -i "s#rootDir = '/vol/fold-grammars/src/'#rootDir = '`pwd`/'#" Misc/Applications/lib/foldGrammars/Settings.pm + #~ - name: execute tests + #~ run: | + #~ cd $GITHUB_WORKSPACE/../fold-grammars + #~ if [[ "${{ matrix.task }}" == "default" ]]; then pushd .; cd Misc/Test-Suite/GeorgStyle/; bash run.sh ../Truth; cd ../StefanStyle/; python test_cofold.py; popd; fi + #~ pushd . + #~ cd Misc/Test-Suite/StefanStyle/ + #~ perl runTests.pl 2 ${{ matrix.task }} + #~ popd #~ cpplint: #~ runs-on: ubuntu-latest From e3d34653be33570b0347a2cfbea37c9383758a5d Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 15:15:47 +0100 Subject: [PATCH 14/26] execute less, be more verbose --- .github/workflows/c-cpp.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 1b4b2bc45..02ec1442d 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -84,14 +84,14 @@ jobs: run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - - name: configure - run: ./configure --prefix $GITHUB_WORKSPACE - - name: patch configuration for OSX - run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf - - name: make - run: make -j 3 - - name: make install - run: sudo make install + #~ - name: configure + #~ run: ./configure --prefix $GITHUB_WORKSPACE + #~ - name: patch configuration for OSX + #~ run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf + #~ - name: make + #~ run: make -j 3 + #~ - name: make install + #~ run: sudo make install - name: debug run: which -a ghc @@ -101,7 +101,7 @@ jobs: cd testdata/paraltest/temp ghc --version cat /Users/runner/.ghc/x86_64-darwin-9.6.2/environments/default - ghc --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain + ghc -v --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain #~ - name: test-mod #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx From 3cfb057ce8a50ae8819aeff101309ea1392322a6 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 15:22:49 +0100 Subject: [PATCH 15/26] add manual lib base installation --- .github/workflows/c-cpp.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 02ec1442d..253b7e632 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -80,6 +80,8 @@ jobs: run: cabal update - name: add random Haskell lib run: cabal install --lib random + - name: add base Haskell lib + run: cabal install --lib base - name: Checkout truth run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite From e5fbf45a0bb2844559cc570615595c32f4c92c81 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 15 Dec 2023 15:46:25 +0100 Subject: [PATCH 16/26] add installation of containers --- .github/workflows/c-cpp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 253b7e632..e2fa1fc4b 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -80,8 +80,8 @@ jobs: run: cabal update - name: add random Haskell lib run: cabal install --lib random - - name: add base Haskell lib - run: cabal install --lib base + - name: add base Haskell lib and containers (prelude, Data.Array) + run: cabal install --lib base containers - name: Checkout truth run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite From 7da9ffa9e19451f9e5de370287587dd35845a0af Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 14:06:31 +0100 Subject: [PATCH 17/26] list installed Haskell packages --- .github/workflows/c-cpp.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index e2fa1fc4b..58ec805c6 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -80,8 +80,8 @@ jobs: run: cabal update - name: add random Haskell lib run: cabal install --lib random - - name: add base Haskell lib and containers (prelude, Data.Array) - run: cabal install --lib base containers + - name: add base Haskell lib (prelude) + run: cabal install --lib base - name: Checkout truth run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite @@ -97,6 +97,8 @@ jobs: - name: debug run: which -a ghc + - name: debug list + run: ghc-pkg list - name: debug1 run: | mkdir -p testdata/paraltest/temp From 29e3a190443c4cd56c3ccd59e4a91ab3de6f6da6 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 14:14:11 +0100 Subject: [PATCH 18/26] explicitely add "-package array" --- .github/workflows/c-cpp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 58ec805c6..9cf6e1dd6 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -105,7 +105,7 @@ jobs: cd testdata/paraltest/temp ghc --version cat /Users/runner/.ghc/x86_64-darwin-9.6.2/environments/default - ghc -v --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain + ghc -package array -v --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain #~ - name: test-mod #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx From 48d6fe5d4f5fd6361cb06d9729e115e26da32721 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 14:20:54 +0100 Subject: [PATCH 19/26] call package array in tool.sh for each GHC make call --- .github/workflows/c-cpp.yml | 232 +++++++++++++++++------------------- testdata/tool.sh | 2 +- 2 files changed, 111 insertions(+), 123 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 9cf6e1dd6..be0897bae 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -15,59 +15,59 @@ on: description: 'Test scenario tags' jobs: - #~ gapc_ubuntu: - #~ needs: cpplint - #~ strategy: - #~ matrix: - #~ # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners - #~ # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/ - #~ # 18.04 burnout: https://github.com/actions/runner-images/issues/6002 - #~ os: [ubuntu-20.04, ubuntu-22.04] - #~ runs-on: ${{ matrix.os }} - #~ steps: - #~ - name: Update apt - #~ run: sudo apt-get update - #~ - name: Install dependencies - #~ run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip + gapc_ubuntu: + needs: cpplint + strategy: + matrix: + # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners + # as of 21st Sep 2021, ubuntu-16.04 is no longer supported by github actions: https://github.blog/changelog/2021-04-29-github-actions-ubuntu-16-04-lts-virtual-environment-will-be-removed-on-september-20-2021/ + # 18.04 burnout: https://github.com/actions/runner-images/issues/6002 + os: [ubuntu-20.04, ubuntu-22.04] + runs-on: ${{ matrix.os }} + steps: + - name: Update apt + run: sudo apt-get update + - name: Install dependencies + run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip - #~ - name: Checkout truth - #~ run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + - name: Checkout truth + run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - #~ - uses: actions/checkout@v3 - #~ - name: configure - #~ run: ./configure --prefix $GITHUB_WORKSPACE - #~ - name: make - #~ run: make -j 2 - #~ - name: make install - #~ run: sudo make install + - uses: actions/checkout@v3 + - name: configure + run: ./configure --prefix $GITHUB_WORKSPACE + - name: make + run: make -j 2 + - name: make install + run: sudo make install - #~ - name: test-mod - #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu - #~ - name: test-mod_outside - #~ run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu - #~ - name: test-regress - #~ run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - #~ - name: test-ambiguity - #~ run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - #~ - name: test-unit - #~ run: make test-unit - #~ # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc - #~ - uses: haskell-actions/setup@v2 - #~ with: - #~ cabal-version: '3.6.2.0' # pin version on 2023-02-09 to enable proper cabal installtion - #~ id: haskell - #~ - name: cabal - #~ run: | - #~ ${{ steps.haskell.outputs.cabal-exe }} v2-update - #~ ${{ steps.haskell.outputs.cabal-exe }} v2-install --lib random + - name: test-mod + run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu + - name: test-mod_outside + run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_ubuntu + - name: test-regress + run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + - name: test-ambiguity + run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + - name: test-unit + run: make test-unit + # we need to install Haskell (especially the System.Random lib) for paralell tests, since we compare Haskell ADP with gapc + - uses: haskell-actions/setup@v2 + with: + cabal-version: '3.6.2.0' # pin version on 2023-02-09 to enable proper cabal installtion + id: haskell + - name: cabal + run: | + ${{ steps.haskell.outputs.cabal-exe }} v2-update + ${{ steps.haskell.outputs.cabal-exe }} v2-install --lib random - #~ - name: test-paral - #~ run: | - #~ package_path=$HOME/.cabal/store/ghc-`${{ steps.haskell.outputs.ghc-exe }} --version | rev | cut -d " " -f 1 | rev`/package.db - #~ GHC="ghc -package-db $package_path" make test-paral + - name: test-paral + run: | + package_path=$HOME/.cabal/store/ghc-`${{ steps.haskell.outputs.ghc-exe }} --version | rev | cut -d " " -f 1 | rev`/package.db + GHC="ghc -package-db $package_path" make test-paral gapc_osx: - #~ needs: cpplint + needs: cpplint strategy: matrix: # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners @@ -86,82 +86,70 @@ jobs: run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - #~ - name: configure - #~ run: ./configure --prefix $GITHUB_WORKSPACE - #~ - name: patch configuration for OSX - #~ run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf - #~ - name: make - #~ run: make -j 3 - #~ - name: make install - #~ run: sudo make install + - name: configure + run: ./configure --prefix $GITHUB_WORKSPACE + - name: patch configuration for OSX + run: gsed -E "s|^YACC = .+$|YACC = /usr/local/opt/bison@2.7/bin/bison|" -i config.mf && gsed -E "s|^SED = .+$|SED = /usr/local/opt/gnu-sed/libexec/gnubin/sed|" -i config.mf && gsed -E "s/ -D_XOPEN_SOURCE=500 / /" -i config.mf && gsed -E "s/ -std=c\+\+17 / -std=c\+\+11 /" -i config.mf + - name: make + run: make -j 3 + - name: make install + run: sudo make install - - name: debug - run: which -a ghc - - name: debug list - run: ghc-pkg list - - name: debug1 - run: | - mkdir -p testdata/paraltest/temp - cd testdata/paraltest/temp - ghc --version - cat /Users/runner/.ghc/x86_64-darwin-9.6.2/environments/default - ghc -package array -v --make ../ElMamunMain.lhs -i.. -hidir ./GHC -odir ./GHC -o ElMamunMain - - #~ - name: test-mod - #~ run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - #~ - name: test-mod_outside - #~ run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx - #~ - name: test-regress - #~ run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - #~ - name: test-ambiguity - #~ run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth - #~ - name: test-unit - #~ run: make test-unit - #~ - name: test-paral - #~ run: make test-paral + - name: test-mod + run: make test-mod TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx + - name: test-mod_outside + run: make -j 2 test-mod_outside TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth TRUTH_SUFFIX=_osx + - name: test-regress + run: make test-regress TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + - name: test-ambiguity + run: make test-ambiguity TRUTH_DIR=$GITHUB_WORKSPACE/../gapc-test-suite/Truth + - name: test-unit + run: make test-unit + - name: test-paral + run: make test-paral - #~ fold-grammars: - #~ needs: cpplint - #~ strategy: - #~ matrix: - #~ task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] - #~ runs-on: ubuntu-latest - #~ steps: - #~ # install gapcs - #~ - name: Update apt - #~ run: sudo apt-get update - #~ - name: Install dependencies - #~ run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython - #~ - uses: actions/checkout@v3 - #~ - name: configure - #~ run: ./configure - #~ - name: make - #~ run: make -j 2 - #~ - name: make install - #~ run: sudo make install + fold-grammars: + needs: cpplint + strategy: + matrix: + task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] + runs-on: ubuntu-latest + steps: + # install gapcs + - name: Update apt + run: sudo apt-get update + - name: Install dependencies + run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython + - uses: actions/checkout@v3 + - name: configure + run: ./configure + - name: make + run: make -j 2 + - name: make install + run: sudo make install - #~ - name: clone fold-grammars - #~ run: git clone --branch master https://github.com/jlab/fold-grammars.git $GITHUB_WORKSPACE/../fold-grammars - #~ - name: configure fold-grammars - #~ run: | - #~ cd $GITHUB_WORKSPACE/../fold-grammars - #~ sed -i "s#bgapDir = '/vol/gapc/'#bgapDir = '/usr/local/'#" Misc/Applications/lib/foldGrammars/Settings.pm - #~ sed -i "s#rootDir = '/vol/fold-grammars/src/'#rootDir = '`pwd`/'#" Misc/Applications/lib/foldGrammars/Settings.pm - #~ - name: execute tests - #~ run: | - #~ cd $GITHUB_WORKSPACE/../fold-grammars - #~ if [[ "${{ matrix.task }}" == "default" ]]; then pushd .; cd Misc/Test-Suite/GeorgStyle/; bash run.sh ../Truth; cd ../StefanStyle/; python test_cofold.py; popd; fi - #~ pushd . - #~ cd Misc/Test-Suite/StefanStyle/ - #~ perl runTests.pl 2 ${{ matrix.task }} - #~ popd + - name: clone fold-grammars + run: git clone --branch master https://github.com/jlab/fold-grammars.git $GITHUB_WORKSPACE/../fold-grammars + - name: configure fold-grammars + run: | + cd $GITHUB_WORKSPACE/../fold-grammars + sed -i "s#bgapDir = '/vol/gapc/'#bgapDir = '/usr/local/'#" Misc/Applications/lib/foldGrammars/Settings.pm + sed -i "s#rootDir = '/vol/fold-grammars/src/'#rootDir = '`pwd`/'#" Misc/Applications/lib/foldGrammars/Settings.pm + - name: execute tests + run: | + cd $GITHUB_WORKSPACE/../fold-grammars + if [[ "${{ matrix.task }}" == "default" ]]; then pushd .; cd Misc/Test-Suite/GeorgStyle/; bash run.sh ../Truth; cd ../StefanStyle/; python test_cofold.py; popd; fi + pushd . + cd Misc/Test-Suite/StefanStyle/ + perl runTests.pl 2 ${{ matrix.task }} + popd - #~ cpplint: - #~ runs-on: ubuntu-latest - #~ steps: - #~ - uses: actions/checkout@v3 - #~ - uses: actions/setup-python@v4 - #~ - run: pip install cpplint - #~ - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/ - #~ - run: cpplint --counting 'detailed' --filter="-build/include_subdir,-readability/casting,-runtime/arrays" --extensions=c,h librna/rnalib.{c,h} - #~ - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" testdata/unittest/* + cpplint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + - run: pip install cpplint + - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" --extensions=cc,hh src/ rtlib/ + - run: cpplint --counting 'detailed' --filter="-build/include_subdir,-readability/casting,-runtime/arrays" --extensions=c,h librna/rnalib.{c,h} + - run: cpplint --recursive --counting 'detailed' --filter="-runtime/references,-build/include_subdir" testdata/unittest/* diff --git a/testdata/tool.sh b/testdata/tool.sh index 70944112f..c495d591d 100644 --- a/testdata/tool.sh +++ b/testdata/tool.sh @@ -19,7 +19,7 @@ build_cpp() build_haskell() { - log ${GHC} --make $LHS_DIR/$1 -i$LHS_DIR -hidir ./GHC -odir ./GHC -o $2 + log ${GHC} -package array --make $LHS_DIR/$1 -i$LHS_DIR -hidir ./GHC -odir ./GHC -o $2 } run_cpp() From afc15cfe077f7d4027c300cfeada84b0edac2d3c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 16:54:10 +0100 Subject: [PATCH 20/26] re-enable special dir's for linker --- config.mf.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/config.mf.in b/config.mf.in index 67cf2dddc..81ff054e6 100644 --- a/config.mf.in +++ b/config.mf.in @@ -84,6 +84,8 @@ LDLIBS = $(RTLIB_LDLIBS) \ RT_LDLIBS = $(GSL_LIBS) -lrna # set to RTLIB_LDFLAGS RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL) \ + -L$(PREFIX)$(LIB_PATH)/$(LIB_RT) \ + -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) \ -L$(PREFIX)$(LIB_PATH) # set to RTLIB_CPPFLAGS RT_CPPFLAGS = $(GSL_CFLAGS) \ From f21b2d8d293385fe6af4fb09b8e25107927a3e04 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 17:12:04 +0100 Subject: [PATCH 21/26] revert paths --- config.mf.in | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config.mf.in b/config.mf.in index 81ff054e6..d07dbd47f 100644 --- a/config.mf.in +++ b/config.mf.in @@ -85,8 +85,7 @@ RT_LDLIBS = $(GSL_LIBS) -lrna # set to RTLIB_LDFLAGS RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL) \ -L$(PREFIX)$(LIB_PATH)/$(LIB_RT) \ - -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) \ - -L$(PREFIX)$(LIB_PATH) + -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) # set to RTLIB_CPPFLAGS RT_CPPFLAGS = $(GSL_CFLAGS) \ -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_GENERAL) \ From bd20ad121483a00cd7776bcbc0e346337b618e4c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 17:12:48 +0100 Subject: [PATCH 22/26] restore \ --- config.mf.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.mf.in b/config.mf.in index d07dbd47f..d71af1adc 100644 --- a/config.mf.in +++ b/config.mf.in @@ -85,7 +85,7 @@ RT_LDLIBS = $(GSL_LIBS) -lrna # set to RTLIB_LDFLAGS RT_LDFLAGS = -L$(PREFIX)$(LIB_PATH)/$(LIB_GENERAL) \ -L$(PREFIX)$(LIB_PATH)/$(LIB_RT) \ - -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) + -L$(PREFIX)$(LIB_PATH)/$(LIB_RNA) \ # set to RTLIB_CPPFLAGS RT_CPPFLAGS = $(GSL_CFLAGS) \ -I$(PREFIX)$(INCLUDE_PATH)/$(LIB_GENERAL) \ From 74e393e63a15ca0f64c7d4853f8eb17f4376b288 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 18:25:05 +0100 Subject: [PATCH 23/26] also expose "containers" --- .github/workflows/c-cpp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index be0897bae..480632ae8 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -80,7 +80,7 @@ jobs: run: cabal update - name: add random Haskell lib run: cabal install --lib random - - name: add base Haskell lib (prelude) + - name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict) run: cabal install --lib base - name: Checkout truth run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite From 3c43062a413c68bd41aa2885e310a40b19b02d51 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 19:23:03 +0100 Subject: [PATCH 24/26] use new branch for Truth --- .github/workflows/c-cpp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 480632ae8..81d2b5aca 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -31,7 +31,7 @@ jobs: run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip - name: Checkout truth - run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + run: git clone --branch osx-12 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - name: configure @@ -83,7 +83,7 @@ jobs: - name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict) run: cabal install --lib base - name: Checkout truth - run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + run: git clone --branch osx-12 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - name: configure From 7b0acfe640df1c3e9fa410f18a2409f85defdf40 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 19:39:16 +0100 Subject: [PATCH 25/26] use master again --- .github/workflows/c-cpp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 81d2b5aca..480632ae8 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -31,7 +31,7 @@ jobs: run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip - name: Checkout truth - run: git clone --branch osx-12 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - name: configure @@ -83,7 +83,7 @@ jobs: - name: add base Haskell lib containers (prelude, Data.Map, Data.Map.Strict) run: cabal install --lib base - name: Checkout truth - run: git clone --branch osx-12 https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite + run: git clone --branch master https://github.com/jlab/gapc-test-suite.git $GITHUB_WORKSPACE/../gapc-test-suite - uses: actions/checkout@v3 - name: configure From 459da01a3de41b77b3039ea626fd1f740fd8b370 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 17 Dec 2023 20:42:16 +0100 Subject: [PATCH 26/26] explicitely expose "containers" haskell module --- testdata/tool.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testdata/tool.sh b/testdata/tool.sh index c495d591d..81760218e 100644 --- a/testdata/tool.sh +++ b/testdata/tool.sh @@ -19,7 +19,7 @@ build_cpp() build_haskell() { - log ${GHC} -package array --make $LHS_DIR/$1 -i$LHS_DIR -hidir ./GHC -odir ./GHC -o $2 + log ${GHC} -package array -package containers --make $LHS_DIR/$1 -i$LHS_DIR -hidir ./GHC -odir ./GHC -o $2 } run_cpp()