Correct integration test suite invocation

amnh · Oct 18, 2022 · 104bc41 · 104bc41
1 parent b38e1e8
commit 104bc41
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Showing 10 changed files with 76 additions and 18 deletions.
diff --git a/.github/workflows/integration-test-suite.yaml b/.github/workflows/integration-test-suite.yaml
@@ -12,6 +12,8 @@ defaults:
 
 env:
   PROJECTFILE: --project-file=cfg/cabal.project.integration
+  TESTDETAILS: --test-show-details=streaming
+  TESTOPTIONS: --test-options="--timeout=30s"
   THISMAINEXE: PhyGraph:phyg
   THISTESTEXE: PHAGE-integration-tests:integration-tests
 
@@ -74,11 +76,11 @@ jobs:
 
       - name: 'Cabal - Build'
         run: |
-          cabal build ${PROJECTFILE} ${THISMAINEXE} ${THISTESTEXE} --only-dependencies
+          cabal build ${THISMAINEXE} ${THISTESTEXE} ${PROJECTFILE} --only-dependencies
 
       - name: 'Cabal - Integration Tests'
         run: |
-          cabal test ${PROJECTFILE} ${THISTESTEXE}
+          cabal test  ${THISTESTEXE} ${PROJECTFILE} ${TESTDETAILS} ${TESTOPTIONS}
 
       - name: Send mail on failure
         if: ${{ failure() }}

diff --git a/cfg/cabal.project.integration b/cfg/cabal.project.integration
@@ -76,6 +76,7 @@ package PHAGE-integration-tests
     tests:             True
     executable-static: False
     optimization: 2
+    flags: -SingleThreaded
 
 
 package PhyGraph
@@ -84,7 +85,7 @@ package PhyGraph
     tests:             False
     executable-static: False
     optimization: 2
-    flags: +SingleThreaded
+    flags: -SingleThreaded
 
 
 ---------------------------------------------------------------------------------

diff --git a/doc/CHANGELOG.md b/doc/CHANGELOG.md
@@ -12,6 +12,7 @@ The changelog is available [on GitHub][2].
   * Major codebase layout rearchitecting
   * Added continuous integration via GitHub Actions
   * Added integration test-suite
+  * Added `PHAGE-timing` library for timing IO operations
 
 
 ## 0.1.0

diff --git a/pkg/PHAGE-timing/CHANGELOG.md b/pkg/PHAGE-timing/CHANGELOG.md
@@ -0,0 +1 @@
+../../doc/CHANGELOG.md
diff --git a/pkg/PHAGE-timing/LICENSE b/pkg/PHAGE-timing/LICENSE
@@ -0,0 +1 @@
+../../doc/LICENSE
diff --git a/pkg/PHAGE-timing/PHAGE-timing.cabal b/pkg/PHAGE-timing/PHAGE-timing.cabal
@@ -0,0 +1,47 @@
+Cabal-Version: 3.0
+Name:          PHAGE-timing
+Version:       0.2.0
+Build-Type:    Simple
+Tested-With:
+  GHC == 9.2.4
+
+Author:        Ward Wheeler <[email protected]>
+Copyright:     (c) 2015-2022 Ward Wheeler
+License:       BSD-3-Clause
+License-File:  LICENSE
+
+Maintainer:    Ward Wheeler <[email protected]>
+Homepage:      https://github.com/wardwheeler/PhyGraph#readme
+Bug-Reports:   https://github.com/wardwheeler/PhyGraph/issues
+
+Extra-Doc-Files:
+  CHANGELOG.md
+  README.md
+
+
+Library
+
+  Build-Depends:
+    base    >= 4.11 && < 5.0,
+    deepseq >= 1.4  && < 2.0,
+
+  Default-Language:
+    Haskell2010
+
+  Exposed-Modules:
+    System.Timing
+
+  Ghc-Options:
+    -O2
+    -- Sanity check warnings:
+    --   1. Fail on a warning
+    --   2. Include all warnings by default
+    --   3. Exclude the undesirable warnings
+    -Werror
+    -Weverything
+    -- Exclusions:
+    -Wno-implicit-prelude
+    -Wno-missing-kind-signatures
+
+  HS-Source-dirs:
+    src
diff --git a/pkg/PHAGE-timing/README.md b/pkg/PHAGE-timing/README.md
@@ -0,0 +1 @@
+../../doc/ReadMe/Timing.md
diff --git a/pkg/PHAGE-timing/Timing.md b/pkg/PHAGE-timing/Timing.md
@@ -0,0 +1 @@
+../../doc/ReadMe/Timing.md
diff --git a/pkg/PhyGraph/System/Timing.hs → pkg/PHAGE-timing/src/System/Timing.hs b/pkg/PhyGraph/System/Timing.hs → pkg/PHAGE-timing/src/System/Timing.hs
@@ -1,5 +1,7 @@
-{-# LANGUAGE BangPatterns #-}
-{-# LANGUAGE Strict       #-}
+{-# Language BangPatterns #-}
+{-# Language DerivingStrategies #-}
+{-# Language Safe #-}
+{-# Language Strict #-}
 
 module System.Timing
   ( CPUTime()
@@ -16,16 +18,16 @@ module System.Timing
   ) where
 
 
-import           Control.DeepSeq
-import           Control.Monad.IO.Class
-import           Data.Foldable
-import           Numeric.Natural
-import           System.CPUTime
+import Control.DeepSeq (NFData(rnf), force)
+import Control.Monad.IO.Class (MonadIO(liftIO))
+import Data.Foldable (fold)
+import Numeric.Natural (Natural)
+import System.CPUTime (getCPUTime)
 
 
 -- | CPU time with picosecond resolution
 newtype CPUTime = CPUTime Natural
-    deriving (Eq, Ord)
+    deriving stock (Eq, Ord)
 
 
 instance NFData CPUTime where
@@ -45,6 +47,7 @@ instance Show CPUTime where
       | x <     day = let (q,r) = x `quotRem`    hour in fold [show q, "h", zeroPad 2 (r `div`  minute ), "min"]
       | otherwise   = let (q,r) = x `quotRem`     day in fold [show q, "d", zeroPad 2 (r `div`    hour ), "hrs"]
       where
+        nSecond :: Natural
         nSecond = 1000
         μSecond = 1000 * nSecond
         mSecond = 1000 * μSecond
@@ -62,9 +65,9 @@ zeroPad k i = replicate (k - length shown) '0' <> shown
 
 timeOp :: (MonadIO m, NFData a) => m a -> m (CPUTime, a)
 timeOp ioa = do
-    t1 <- liftIO getCPUTime
-    a  <- force <$> ioa
-    t2 <- liftIO getCPUTime
+    !t1 <- liftIO getCPUTime
+    !a  <- force <$> ioa
+    !t2 <- liftIO getCPUTime
     let t = CPUTime . fromIntegral $ t2 - t1
     pure (t, a)
 
@@ -78,15 +81,15 @@ fromPicoseconds = CPUTime
 
 
 fromMicroseconds :: Natural -> CPUTime
-fromMicroseconds = CPUTime . (*1000000)
+fromMicroseconds = CPUTime . (* 1000000)
 
 
 fromMilliseconds :: Natural -> CPUTime
-fromMilliseconds = CPUTime . (*1000000000)
+fromMilliseconds = CPUTime . (* 1000000000)
 
 
 fromSeconds :: Natural -> CPUTime
-fromSeconds = CPUTime . (*1000000000000)
+fromSeconds = CPUTime . (* 1000000000000)
 
 
 toPicoseconds :: CPUTime -> Natural

diff --git a/pkg/PhyGraph/PhyGraph.cabal b/pkg/PhyGraph/PhyGraph.cabal
@@ -145,6 +145,7 @@ executable phyg
   build-depends:
     alphabet,
     dynamic-character,
+    PHAGE-timing,
     PhyloLib,
     tcm,
     base >=4.10,
@@ -219,7 +220,6 @@ executable phyg
     Search.SwapMaster 
     Search.WagnerBuild
     Support.Support
-    System.Timing
     Commands.Transform
     Types.DistanceTypes
     Types.Types