Merge pull request cyclus#1 from bam241/fix

fix reactor compilation

.gitignore

@@ -11,6 +11,6 @@ rs.cred
 *.dat
 tests/run_inputs.py
 cyclus.sqlite
-cycamore_version.h
+recyle_version.h
 *.sqlite
-src/version.cc.in
+src/version.cc.in

CMakeLists.txt

@@ -297,6 +297,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     TARGET_LINK_LIBRARIES(recycle_unit_tests
         dl
         ${LIBS}
+        recycle
         ${CYCLUS_TEST_LIBRARIES}
         )
 

CONTRIBUTING.rst

@@ -67,7 +67,7 @@ You can run the tests yourself using:
 
     .. code-block:: bash
 
-      $ cycamore_unit_tests
+      $ recyle_unit_tests
 
 Cautions
 ========

DEPENDENCIES.rst

@@ -127,7 +127,7 @@ installation procedure also assumes that you have root access to you computer.
 .. _`Cyclus Homepage`: http://fuelcycle.org/
 .. _`Cyclus User Guide`: http://fuelcycle.org/user/index.html
 .. _`Cyclus repo`: https://github.com/cyclus/cyclus
-.. _`Cycamore Repo`: https://github.com/cyclus/cycamore
+.. _`Cycamore Repo`: https://github.com/cyclus/recyle
 .. _Anaconda: https://www.continuum.io/downloads
 .. _miniconda: http://conda.pydata.org/miniconda.html
 .. _`dependency installation documentation`: https://github.com/cyclus/cyclus/blob/develop/DEPENDENCIES.rst

README.rst

@@ -63,10 +63,10 @@ Quick Cycamore Installation
 Assuming you have the dependencies installed correctly, installing Cyclus using
 github is fairly straightforward:
 
-- Clone the Cyclus Repo: ``git clone https://github.com/cyclus/cycamore.git``,
+- Clone the Cyclus Repo: ``git clone https://github.com/cyclus/recyle.git``,
 
 - to install Cyclus locally (in ``~/.local/``) just run: ``python install.py``
-  from cycamore folder,
+  from recyle folder,
 
 - finally, add the following Cyclus installation path (``~/.local/cyclus``) to
   the **bottom** on your ``$PATH``.
@@ -84,7 +84,7 @@ our tests). You can run the tests yourself via:
 
 .. code-block:: bash
 
-    $ cycamore_unit_tests
+    $ recyle_unit_tests
 
 ******************************
 Contributing
@@ -99,7 +99,7 @@ to contribute into Cyclus, please follow this procedure:
 
 #. Implement your modification of the Cycamore source code,
 
-#. Submit a Pull request into ``cycamore/master`` branch,
+#. Submit a Pull request into ``recyle/master`` branch,
 
 #. Wait for reviews/merge (the Puller cannot be the Merger).
 
@@ -109,7 +109,7 @@ You may also want to read our `Contribution Guidelines <CONTRIBUTING.rst>`_.
 .. _`Cyclus Homepage`: http://fuelcycle.org/
 .. _`Cyclus User Guide`: http://fuelcycle.org/user/index.html
 .. _`Cyclus repo`: https://github.com/cyclus/cyclus
-.. _`Cycamore Repo`: https://github.com/cyclus/cycamore
+.. _`Cycamore Repo`: https://github.com/cyclus/recyle
 .. _`INSTALL`: INSTALL.rst
 .. _`CONTRIBUTING`: CONTRIBUTING.rst
 

circle.yml

@@ -5,7 +5,7 @@ jobs:
     build:
         docker:
             - image: cyclus/cyclus:latest
-        working_directory: ~/cycamore
+        working_directory: ~/recyle
         steps:
             # Ensure your image has git (required by git to clone via SSH) so that CircleCI can clone your repo
             - run: apt-get -qq update; apt-get -y install git openssh-client
@@ -40,7 +40,7 @@ jobs:
                   - v1-repo-{{ checksum ".circle-sha" }}
             - run:
                 name: Unit Test
-                command: /root/.local/bin/cycamore_unit_tests; exit $?
+                command: /root/.local/bin/recyle_unit_tests; exit $?
     nosetest:
         docker:
             - image: cyclus/cyclus:latest
@@ -57,14 +57,14 @@ jobs:
                 command: pip install nose
             - run:
                 name: Nosetests
-                command: nosetests -w ~/cycamore/tests; exit $?
+                command: nosetests -w ~/recyle/tests; exit $?
 
 
     # Update docker container
     deploy: # Cycamore -> Cycamore:latest
         docker:
             - image: circleci/ruby:2.4-node
-        working_directory: ~/cycamore
+        working_directory: ~/recyle
         steps:
             - checkout
             - run:
@@ -77,15 +77,15 @@ jobs:
                     docker login -u $DOCKER_USER -p $DOCKER_PASS
             - run:
                 name: Build Docker container
-                command: docker build --rm=false -t cyclus/cycamore:latest .
+                command: docker build --rm=false -t cyclus/recyle:latest .
             - run:
                 name: Push on DockerHub
-                command: docker push cyclus/cycamore:latest # push to docker depot
+                command: docker push cyclus/recyle:latest # push to docker depot
 
     deploy_stable: # Cycamore:stable
         docker:
             - image: circleci/ruby:2.4-node
-        working_directory: ~/cycamore
+        working_directory: ~/recyle
         steps:
             - checkout
             - run:
@@ -98,17 +98,17 @@ jobs:
                   docker login -u $DOCKER_USER -p $DOCKER_PASS
             - run:
                 name: Build Docker container
-                command: docker build -t cyclus/cycamore:stable .
+                command: docker build -t cyclus/recyle:stable .
             - run:
                 name: Push on DockerHub
-                command: docker push cyclus/cycamore:stable # push to docker depot
+                command: docker push cyclus/recyle:stable # push to docker depot
 
 
     # Debian package generation (on master update)
     deb_generation:
         docker:
             - image: circleci/ruby:2.4-node
-        working_directory: ~/cycamore
+        working_directory: ~/recyle
         steps:
             - checkout
             - setup_remote_docker

conda-recipe/meta.yaml

@@ -1,11 +1,11 @@
 package:
-  name: cycamore
+  name: recyle
   version: 0.0
 
 # Only use fn and url for polyphemus compatability
 source:
-  fn: cycamore-src.tar.gz # ["TRAVIS" not in environ] 
-  url: https://github.com/cyclus/cycamore/archive/develop.tar.gz # ["TRAVIS" not in environ]
+  fn: recyle-src.tar.gz # ["TRAVIS" not in environ] 
+  url: https://github.com/cyclus/recyle/archive/develop.tar.gz # ["TRAVIS" not in environ]
   path: ..  # ["TRAVIS" in environ]
 
 requirements:

conda-recipe/post-link.sh

@@ -1,4 +1,4 @@
-# This script replaces the cycamore_unit_tests commands with a simple
+# This script replaces the recyle_unit_tests commands with a simple
 # wrapper that will modify the user's environment as needed to point  
 # cyclus-sepcific envrionment variables to the conda install location $PREFIX.
 # Conda packaging has three phases which come to a head here.
@@ -18,7 +18,7 @@ echo "post-link.sh, PREFIX: $PREFIX"
 # The library path modifications are here because cyclus installs 
 # libgtest and libbaseagentunittests into the lib/cyclus directory.
 # We make this directory the last possible location to be searched.
-mv $PREFIX/bin/cycamore_unit_tests $PREFIX/bin/cycamore_unit_tests_base
+mv $PREFIX/bin/recyle_unit_tests $PREFIX/bin/recyle_unit_tests_base
 echo "#!/bin/bash
 export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$PREFIX/lib/cyclus\"
 export DYLD_FALLBACK_LIBRARY_PATH=\"\$DYLD_FALLBACK_LIBRARY_PATH:$PREFIX/lib/cyclus\"
@@ -29,6 +29,6 @@ fi
 if [ -z \"\$CYCLUS_RNG_SCHEMA\" ]; then
   export CYCLUS_RNG_SCHEMA=\"$PREFIX/share/cyclus/cyclus.rng.in\"
 fi
-$PREFIX/bin/cycamore_unit_tests_base \$*
-" > $PREFIX/bin/cycamore_unit_tests
-chmod 755 $PREFIX/bin/cycamore_unit_tests
+$PREFIX/bin/recyle_unit_tests_base \$*
+" > $PREFIX/bin/recyle_unit_tests
+chmod 755 $PREFIX/bin/recyle_unit_tests

docker/deb-ci/Dockerfile_template

@@ -35,10 +35,10 @@ RUN wget -r --no-parent -A 'cyclus_1.5.0_*_ubuntu.CYCAMORE_UBUNTU_MAJOR_VERSION.
 run mv dory.fuelcycle.org:4848/* ./; rm -rf dory.fuelcycle.org:4848
 RUN dpkg -i cyclus_1.5.0_*_ubuntu.CYCAMORE_UBUNTU_MAJOR_VERSION.04.deb
 
-COPY . /cycamore 
-WORKDIR cycamore
+COPY . /recyle 
+WORKDIR recyle
 RUN mkdir -p deb
-WORKDIR /cycamore/deb
+WORKDIR /recyle/deb
 RUN cmake -DCPACK_PACKAGING_INSTALL_PREFIX=/usr/local -DCMAKE_INSTALL_PREFIX=/usr/local -DCPACK_HASH_NAME=CYCAMORE_REPO_HASH -DCPACK_SYSTEM_NAME=ubuntu.CYCAMORE_UBUNTU_MAJOR_VERSION.04 ..
 
 # Build the deb file in the docker container

docker/deb-ci/build_upload_deb.sh

@@ -11,6 +11,6 @@ sed -i s/CYCAMORE_REPO_HASH/`git rev-parse --short HEAD`/g Dockerfile
 
 docker build -t deb/ubuntu-${1} . # build cyclus against ubuntu 14.04 in the docker container
 docker create --name=deb-${1}.04 deb/ubuntu-${1} # build deb in docker
-docker cp deb-${1}.04:/cycamore/deb ./ # extract deb
-scp ./deb/cycamore_*_ubuntu.${1}.04.deb [email protected]:./cyclus-deb/ # push the deb on dory
+docker cp deb-${1}.04:/recyle/deb ./ # extract deb
+scp ./deb/recyle_*_ubuntu.${1}.04.deb [email protected]:./cyclus-deb/ # push the deb on dory
 rm -rf deb  # clean the deb folder

docker/master-ci/Dockerfile

@@ -1,7 +1,7 @@
 FROM cyclus/cyclus:latest
 
-COPY . /cycamore
-WORKDIR /cycamore
+COPY . /recyle
+WORKDIR /recyle
 ENV PATH="/root/.local/bin:${PATH}"
 RUN python install.py -j 2 --build-type=Release \
     -DBLAS_LIBRARIES="/opt/conda/lib/libblas.so" \

docker/release-ci/Dockerfile

@@ -1,10 +1,10 @@
 
 FROM cyclus/cyclus:stable
 
-COPY . /cycamore
-WORKDIR /cycamore
+COPY . /recyle
+WORKDIR /recyle
 RUN mkdir Release
-WORKDIR /cycamore/Release
+WORKDIR /recyle/Release
 RUN cmake .. -DCMAKE_BUILD_TYPE=Release
 RUN make -j2 && make install
 

tests/README.rst

@@ -10,7 +10,7 @@ Dependencies
 Running Tests
 -------------
 
-To run the regression tests from the cycamore/tests:
+To run the regression tests from the recyle/tests:
 
 .. code-block:: bash
 
@@ -43,13 +43,13 @@ Next, rename the databases:
 
 .. code-block:: bash
 
-  $ rename 's/^[^_]*_[^_]*_(.*)/<cyclus version>_<cycamore version>_$1/' *.h5
+  $ rename 's/^[^_]*_[^_]*_(.*)/<cyclus version>_<recyle version>_$1/' *.h5
 
 where
 
 * <cyclus version> is replaced by the current version tag name for cyclus
   (e.g. v0.1)
-* <cycamore version> is replaced by the current version tag name for cycamore
+* <recyle version> is replaced by the current version tag name for recyle
   (e.g. v0.1)
 
 so that, using the above examples, the command is

tests/input/dynamic_capacitated.xml

@@ -8,10 +8,10 @@
   <solver><config><coin-or><timeout>100</timeout><verbose>1</verbose></coin-or></config></solver></control>
 
   <archetypes>
-    <spec><lib>cycamore</lib><name>Sink</name></spec>
-    <spec><lib>cycamore</lib><name>Source</name></spec>
+    <spec><lib>recyle</lib><name>Sink</name></spec>
+    <spec><lib>recyle</lib><name>Source</name></spec>
     <spec><lib>agents</lib><name>NullRegion</name></spec>
-    <spec><lib>cycamore</lib><name>DeployInst</name></spec>
+    <spec><lib>recyle</lib><name>DeployInst</name></spec>
   </archetypes>
 
   <facility>

tests/input/growth.xml

@@ -9,19 +9,19 @@
 
   <archetypes>
     <spec>
-      <lib>cycamore</lib>
+      <lib>recyle</lib>
       <name>Source</name>
     </spec>
     <spec>
-      <lib>cycamore</lib>
+      <lib>recyle</lib>
       <name>Sink</name>
     </spec>
     <spec>
-      <lib>cycamore</lib>
+      <lib>recyle</lib>
       <name>GrowthRegion</name>
     </spec>
     <spec>
-      <lib>cycamore</lib>
+      <lib>recyle</lib>
       <name>ManagerInst</name>
     </spec>
   </archetypes>

tests/test_regression.py

@@ -116,8 +116,8 @@ def __init__(self, *args, **kwargs):
     def setUp(self):
         super(_PhysorEnrichment, self).setUp()
         tbl = self.agent_entry
-        self.rx_id = self.find_ids(":cycamore:Reactor", tbl)
-        self.enr_id = self.find_ids(":cycamore:Enrichment", tbl)
+        self.rx_id = self.find_ids(":recyle:Reactor", tbl)
+        self.enr_id = self.find_ids(":recyle:Enrichment", tbl)
 
     def test_deploy(self):
         assert_equal(len(self.rx_id), 2)
@@ -190,9 +190,9 @@ def setUp(self):
 
         # identify each reactor and supplier by id
         tbl = self.agent_entry
-        rx_id = self.find_ids(":cycamore:Reactor", tbl)
+        rx_id = self.find_ids(":recyle:Reactor", tbl)
         self.r1, self.r2, self.r3 = tuple(rx_id)
-        s_id = self.find_ids(":cycamore:Source", tbl)
+        s_id = self.find_ids(":recyle:Source", tbl)
         self.smox = self.transactions[0]["SenderId"]
         s_id.remove(self.smox)
         self.suox = s_id[0]
@@ -294,8 +294,8 @@ def setUp(self):
         self.depl_time = self.to_ary(self.agent_entry, "EnterTime")
         self.exit_time = self.to_ary(self.agent_exit, "ExitTime")
         self.exit_ids = self.to_ary(self.agent_exit, "AgentId")
-        self.source_id = self.find_ids(":cycamore:Source", self.agent_entry)
-        self.sink_id = self.find_ids(":cycamore:Sink", self.agent_entry)
+        self.source_id = self.find_ids(":recyle:Source", self.agent_entry)
+        self.sink_id = self.find_ids(":recyle:Sink", self.agent_entry)
 
         # Check transactions
         self.sender_ids = self.to_ary(self.transactions, "SenderId")