From 1808f0957c0894ecc184edf601ec97c43ce0c50e Mon Sep 17 00:00:00 2001
From: Aaron Kollasch <aaron@kollasch.dev>
Date: Fri, 20 Jan 2023 18:02:59 -0500
Subject: [PATCH 1/3] Reduce protein.sh test precision

Don't check last decimal digit of couplings output
---
 tests/protein.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 tests/protein.sh

diff --git a/tests/protein.sh b/tests/protein.sh
old mode 100644
new mode 100755
index eead404..d607b9f
--- a/tests/protein.sh
+++ b/tests/protein.sh
@@ -9,8 +9,12 @@ tmpfile2="$(mktemp /tmp/evcouplings.XXXXXX)"
 echo "$tmpfile2"
 ../bin/plmc -c "$tmpfile" --save-weights "$tmpfile2" -le 16.0 -lh 0.01 -m 100 -g -f DYR_ECOLI ../example/protein/DHFR.a2m
 
+# Compare couplings lines except for last decimal digit
 comp_value=0
-diff --brief "$tmpfile" DHFR.couplings || comp_value=$?
+diff --brief -L "$tmpfile" -L DHFR.couplings \
+    <(while IFS= read -r line; do echo "${line%?}"; done < "$tmpfile") \
+    <(while IFS= read -r line; do echo "${line%?}"; done < DHFR.couplings) ||
+    comp_value=$?
 
 weights_comp=0
 diff --brief "$tmpfile2" DHFR_weights_raw.txt || weights_comp=$?
@@ -41,8 +45,12 @@ tmpfile="$(mktemp /tmp/evcouplings.XXXXXX)"
 tmpfile2="$(mktemp /tmp/evcouplings.XXXXXX)"
 ../bin/plmc -c "$tmpfile" -le 16.0 -lh 0.01 -m 100 -g -f DYR_ECOLI -w DHFR_weights_raw.txt --save-weights "$tmpfile2" ../example/protein/DHFR.a2m
 
+# Compare couplings lines except for last decimal digit
 comp_value=0
-diff --brief "$tmpfile" DHFR.couplings || comp_value=$?
+diff --brief -L "$tmpfile" -L DHFR.couplings \
+    <(while IFS= read -r line; do echo "${line%?}"; done < "$tmpfile") \
+    <(while IFS= read -r line; do echo "${line%?}"; done < DHFR.couplings) ||
+    comp_value=$?
 
 weights_comp=0
 diff --brief "$tmpfile2" DHFR_weights_raw.txt || weights_comp=$?

From 6d3f6fd2bea78fcf1a9c4bf715cb55ab15851f82 Mon Sep 17 00:00:00 2001
From: Aaron Kollasch <aaron@kollasch.dev>
Date: Fri, 20 Jan 2023 18:03:38 -0500
Subject: [PATCH 2/3] Enable protein.sh test on gh actions

---
 .github/workflows/main.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a94364f..99e4e40 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -56,8 +56,8 @@ jobs:
             *-apple-darwin) make all-mac-openmp ;;
           esac
 
-      # - name: Run tests (skip as this takes too long)
-      #   run: |
-      #     pwd
-      #     cd tests
-      #     bash protein.sh
+      - name: Run tests (skip as this takes too long)
+        run: |
+          pwd
+          cd tests
+          bash protein.sh

From 6d64d360745dd9f7683350f2789f04c5aae59344 Mon Sep 17 00:00:00 2001
From: Aaron Kollasch <aaron@kollasch.dev>
Date: Fri, 20 Jan 2023 22:26:09 -0500
Subject: [PATCH 3/3] Move end-to-end test to optional gh action

---
 .github/workflows/end_to_end.yml | 63 ++++++++++++++++++++++++++++++++
 .github/workflows/main.yml       | 12 +++---
 2 files changed, 69 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/end_to_end.yml

diff --git a/.github/workflows/end_to_end.yml b/.github/workflows/end_to_end.yml
new file mode 100644
index 0000000..898cd4e
--- /dev/null
+++ b/.github/workflows/end_to_end.yml
@@ -0,0 +1,63 @@
+---
+name: end-to-end run
+
+# Controls when the action will run.
+on:
+  # # Triggers the workflow on push or pull request events but only for the master branch
+  # # don't trigger on push
+  # push:
+  #   branches: [ master ]
+  # pull_request:
+  #   branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  tests:
+    name: "test ${{ matrix.job.target }} (${{ matrix.job.os }})"
+    runs-on: "${{ matrix.job.os }}"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        job:
+          - { target: x86_64-apple-darwin         , os: macos-latest                   }
+          - { target: x86_64-unknown-linux-gnu    , os: ubuntu-latest, use-cross: true }
+
+    steps:
+      - name: Checkout source code
+        uses: "actions/checkout@v3"
+        with:
+          submodules: 'recursive'
+
+      - name: Install prerequisites
+        env:
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: 1
+        run: |
+          case ${{ matrix.job.target }} in
+            *-unknown-linux-*) sudo apt-get -y update ; sudo apt-get -y install libomp-dev ;;
+            *-apple-darwin) brew install gcc libomp; ;;
+          esac
+
+      - name: Compile default
+        run: |
+          case ${{ matrix.job.target }} in
+            *-unknown-linux-*) make all ;;
+            *-apple-darwin) make all-mac ;;
+          esac
+
+      - name: Compile multicore
+        run: |
+          case ${{ matrix.job.target }} in
+            *-unknown-linux-*) make all-openmp ;;
+            *-apple-darwin) make all-mac-openmp ;;
+          esac
+
+      - name: Run end-to-end test
+        run: |
+          pwd
+          cd tests
+          bash protein.sh
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 99e4e40..3802d0d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,7 +16,7 @@ on:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   tests:
-    name: "run_tests ${{ matrix.job.target }} (${{ matrix.job.os }})"
+    name: "compile ${{ matrix.job.target }} (${{ matrix.job.os }})"
     runs-on: "${{ matrix.job.os }}"
 
     strategy:
@@ -56,8 +56,8 @@ jobs:
             *-apple-darwin) make all-mac-openmp ;;
           esac
 
-      - name: Run tests (skip as this takes too long)
-        run: |
-          pwd
-          cd tests
-          bash protein.sh
+      # - name: Run tests (skip as this takes too long)
+      #   run: |
+      #     pwd
+      #     cd tests
+      #     bash protein.sh