Merge pull request #108 from OpenTreeOfLife/development

Development

.github/workflows/build.yml

@@ -0,0 +1,124 @@
+name: Build and test
+
+on:
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+    - "*"
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        name: [ubuntu-gcc-9,
+               ubuntu-gcc-10,
+#               ubuntu-clang-9,
+#               macos-xcode-12.3,
+               ]
+
+        include:
+          - name: ubuntu-gcc-9
+            os: ubuntu-20.04
+            compiler: gcc
+            version: "9"
+
+          - name: ubuntu-gcc-10
+            os: ubuntu-20.04
+            compiler: gcc
+            version: "10"
+
+#          - name: ubuntu-clang-9
+#            os: ubuntu-20.04
+#            compiler: clang
+#            version: "9"
+
+#          - name: macos-xcode-12.3
+#            os: macos-latest
+#            compiler: xcode
+#            version: "12.3"
+
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt install -y ccache libboost-all-dev
+        sudo rm -rf /usr/local/share/boost
+        if [ "${{ matrix.compiler }}" = "gcc" ]; then
+          sudo apt-get install -y g++-${{ matrix.version }}
+          echo "CC=ccache gcc-${{ matrix.version }}" >> $GITHUB_ENV
+          echo "CXX=ccache g++-${{ matrix.version }}" >> $GITHUB_ENV
+        else
+          sudo apt-get install -y clang-${{ matrix.version }}
+          echo "CC=ccache clang-${{ matrix.version }}" >> $GITHUB_ENV
+          echo "CXX=ccache clang++-${{ matrix.version }}" >> $GITHUB_ENV
+        fi
+
+    - name: Install (macOS)
+      if: runner.os == 'macOS'
+      run: |
+          brew install pkg-config boost ccache coreutils
+          echo "DEVELOPER_DIR=/Applications/Xcode_${{ matrix.version }}.app/Contents/Developer" >> $GITHUB_ENV
+          echo "CC=ccache clang" >> $GITHUB_ENV
+          echo "CXX=ccache clang++" >> $GITHUB_ENV
+          ccache --set-config=cache_dir=$HOME/.ccache
+
+    - name: Install meson
+      run: |
+        python3 -mpip install meson ninja
+
+    # Caches for different branches are isolated, so we don't need to put the branch name into the key.
+
+    - name: Prepare ccache timestamp
+      id: ccache_cache_timestamp
+      run: |
+        if [ "$RUNNER_OS" = "Linux" ]; then
+          stamp=$(date '+%s')
+        else
+          stamp=$(gdate '+%s')
+        fi
+        echo "${stamp}"
+        echo "::set-output name=timestamp::${stamp}"
+
+    - name: ccache cache files
+      uses: actions/cache@v2
+      with:
+         path: ~/.ccache
+         key: ${{ matrix.name }}-ccache-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
+         restore-keys: |
+           ${{ matrix.name }}-ccache-
+
+    - name: build restbed
+      run: |
+        cd
+        git clone --recursive https://github.com/corvusoft/restbed.git
+        mkdir restbed/build
+        ( cd restbed/build ; cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DBUILD_TESTS=NO -DBUILD_SSL=NO -DCMAKE_INSTALL_PREFIX="$HOME/local/" .. ; make ; make install )
+        echo "CPPFLAGS=-I${HOME}/local/include" >> $GITHUB_ENV
+        echo "LDFLAGS=-L${HOME}/local/lib -L${HOME}/local/library" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=${HOME}/local/lib:${HOME}/local/library:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+    - name: Configure otcetera
+      run: |
+        cd ${GITHUB_WORKSPACE}
+        meson build --prefix=$HOME/local --buildtype=release ${ARGS}
+
+    - name: Build otcetera
+      run: |
+        ccache -p
+        ninja -C build install -j4
+        ccache -s
+
+    - name: Run otcetera tests
+      run: |
+        python3 -mpip install requests
+        ninja -C build test
+
+

LICENSE

@@ -4,7 +4,7 @@ flag, then you can choose between a GPL or BSD license.
 If you use the --with-webservices=yes configure flag, only the
     GPL is permitted.
 
-Copyright (c) 2015-2017 Mark T. Holder and Benjamin D. Redelings
+Copyright (c) 2015-2020 Mark T. Holder and Benjamin D. Redelings
 All rights reserved.
 
 otcetera builds upon NCL and is distributed under the same license:

data/synth-setups/synth-2/expectedws/node_lookup/1/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'asdf' was not found!",
+  "unknown": {
+    "asdf": "unknown_id"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/1/expected_code.txt

@@ -0,0 +1 @@
+400

data/synth-setups/synth-2/expectedws/node_lookup/1/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "asdf"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/2/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott111111111111111111111111111111' was not found!",
+  "unknown": {
+    "ott111111111111111111111111111111": "unknown_id"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/2/expected_code.txt

@@ -0,0 +1 @@
+400

data/synth-setups/synth-2/expectedws/node_lookup/2/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "ott111111111111111111111111111111"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/3/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott11111111' was not found!",
+  "unknown": {
+    "ott11111111": "invalid_ott_id"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/3/expected_code.txt

@@ -0,0 +1 @@
+400

data/synth-setups/synth-2/expectedws/node_lookup/3/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "ott11111111"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/4/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott671092' was not found!",
+  "unknown": {
+    "ott671092": "pruned_ott_id"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/4/expected_code.txt

@@ -0,0 +1 @@
+400

data/synth-setups/synth-2/expectedws/node_lookup/4/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "ott671092"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/5/expected.json

@@ -0,0 +1,9 @@
+{
+  "broken": {
+    "ott1007062": "ott304358"
+  },
+  "newick": "((((((((((((((Streptophyta_ott916750)Embryophyta_ott56610)Tracheophyta_ott10210)Euphyllophyta_ott1007992)Spermatophyta_ott10218)Magnoliophyta_ott99252)Mesangiospermae_ott5298374)Liliopsida_ott1058517)Petrosaviidae_ott5308424)Asparagales_ott557124)Amaryllidaceae_ott258473)Amaryllidoideae_ott267867)Archaeplastida_ott5268475)mrcaott56601ott4671788,(((((((((((((((((((Aves_ott81461)Coelurosauria_ott664351)Theropoda_ott664350)Saurischia_ott90223)Dinosauria_ott90215)Archosauria_ott335588)Archelosauria_ott4947372)'Sauria (order in Opisthokonta) ott329823')Sauropsida_ott639642)Amniota_ott229560)Tetrapoda_ott229562)Dipnotetrapodomorpha_ott4940726)Sarcopterygii_ott458402)Euteleostomi_ott114654)Teleostomi_ott114656)'Gnathostomata (superclass in phylum Chordata) ott278114')'Vertebrata (subphylum in Opisthokonta) ott801601')'Craniata (subphylum in Deuterostomia) ott947318')Chordata_ott125642)Deuterostomia_ott147604)Eukaryota_ott304358;",
+  "supporting_studies": [
+    "xx_2@Tree1"
+  ]
+}

data/synth-setups/synth-2/expectedws/node_lookup/5/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "ott1007062"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/6/expected.json

@@ -0,0 +1,8 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott671092' was not found!",
+  "unknown": {
+    "asdf": "unknown_id",
+    "ott11111111": "invalid_ott_id",
+    "ott671092": "pruned_ott_id"
+  }
+}

data/synth-setups/synth-2/expectedws/node_lookup/6/expected_code.txt

@@ -0,0 +1 @@
+400

data/synth-setups/synth-2/expectedws/node_lookup/6/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott916750", "ott81461", "asdf", "ott11111111", "ott671092", "ott1007062"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

expected/solve-subproblem/is-clade-1/output

@@ -1 +1 @@
-((((A1_ott1,(C1_ott5,C2_ott6)C_ott12),A2_ott2)A_ott10,(B1_ott3,B2_ott4)B_ott11)AB_ott20,D_ott7)root_ott100;
+(((((C1_ott5,C2_ott6)C_ott12,A1_ott1),A2_ott2)A_ott10,(B1_ott3,B2_ott4)B_ott11)AB_ott20,D_ott7)root_ott100;

expected/solve-subproblem/is-naming1/output

@@ -1 +1 @@
-((A1_ott1,A2_ott2)A_ott10,((B1_ott3,C1_ott5),(B2_ott4,C2_ott6))B_ott11)root_ott100;
+(((B1_ott3,C1_ott5),(B2_ott4,C2_ott6))B_ott11,(A1_ott1,A2_ott2)A_ott10)root_ott100;

expectedws/node_lookup/1/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'asdf' was not found!",
+  "unknown": {
+    "asdf": "unknown_id"
+  }
+}

expectedws/node_lookup/1/expected_code.txt

@@ -0,0 +1 @@
+400

expectedws/node_lookup/1/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott1", "ott13", "asdf"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

expectedws/node_lookup/2/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott111111111111111111111111111111' was not found!",
+  "unknown": {
+    "ott111111111111111111111111111111": "unknown_id"
+  }
+}

expectedws/node_lookup/2/expected_code.txt

@@ -0,0 +1 @@
+400

expectedws/node_lookup/2/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott1", "ott13", "ott111111111111111111111111111111"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

expectedws/node_lookup/3/expected.json

@@ -0,0 +1,6 @@
+{
+  "message": "[/v3/tree_of_life/induced_subtree] Error: node_id 'ott11111111' was not found!",
+  "unknown": {
+    "ott11111111": "invalid_ott_id"
+  }
+}

expectedws/node_lookup/3/expected_code.txt

@@ -0,0 +1 @@
+400

expectedws/node_lookup/3/method.json

@@ -0,0 +1,10 @@
+{
+  "url_fragment": "v3/tree_of_life/induced_subtree",
+  "verb": "POST",
+  "arguments": {
+    "node_ids": ["ott1", "ott13", "ott11111111"],
+    "height_limit": 10,
+    "label_format": "name_and_id",
+    "format": "newick"
+  }
+}

meson.build

@@ -2,6 +2,7 @@ project('otcetera', ['cpp'],
 	version: '0.0.01-dev',
 	default_options: [
 	  'buildtype=release',
+          'b_ndebug=if-release',
 	  'cpp_std=c++17',
           'warning_level=3'
 	],
@@ -69,7 +70,16 @@ summary({'webservices': get_option('webservices'),
 summary({'prefix': get_option('prefix'),
         },section: 'Directories')
 
+assertions_off = get_option('b_ndebug') == 'true' or (get_option('b_ndebug') == 'if-release' and
+                                                      (get_option('buildtype') == 'release' or
+                                                       get_option('buildtype') == 'plain')
+                                                     )
+assertions_enabled = 'enabled'
+if assertions_off
+  assertions_enabled = 'disabled'
+endif
+
 summary({'optimization': get_option('optimization'),
-         'b_ndebug': get_option('b_ndebug'),
          'debug': get_option('debug'),
+         'assertions': assertions_enabled,
         },section: 'Build')