Merge pull request #3 from LLNL/master

master merge

.travis.yml

@@ -7,6 +7,7 @@ install:
   - "pip install --upgrade pip"
   - "pip install cryptography"
   - "pip install -r requirements.txt"
+  - "pip install -r workflows/feature_demo/requirements.txt"
   - "pip install -e ."
   - "pip install -r requirements/mysql.txt"
   - "pip install --upgrade sphinx"

CHANGELOG.md

@@ -4,6 +4,26 @@ All notable changes to Merlin will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.4] - 2019-12-04
+
+### Added
+- `requirements.txt` files and `scripts` directories for internal workflow examples.
+
+### Fixed
+- Added missing dependency `tabulate` to `release.txt`.
+
+## [1.0.3] - 2019-12-04
+
+### Added
+Added the requirements files to the MANIFEST.in file for source 
+distributions.
+
+## [1.0.2] - 2019-12-04
+Negligible changes related to PyPI.
+
+## [1.0.1] - 2019-12-04
+Negligible changes related to PyPI.
+
 ## [1.0.0] - 2019-11-19
 First public release. See the docs and merlin -h for details.
 Here are some highlights.

MANIFEST.in

@@ -2,3 +2,5 @@ prune docs
 prune tests
 include workflows/*
 include merlin/data/*
+include requirements.txt
+include requirements/*

merlin/__init__.py

@@ -38,7 +38,7 @@
 import sys
 
 
-__version__ = "1.0.2"
+__version__ = "1.0.4"
 VERSION = __version__
 PATH_TO_PROJ = os.path.join(os.path.dirname(__file__), "")
 

requirements/release.txt

@@ -3,10 +3,12 @@ celery[redis]>=4.3.0
 coloredlogs
 cryptography
 importlib_resources; python_version < '3.7'
+# maestrowf>=1.1.5
 numpy
 parse
 psutil>=5.1.0
 pyyaml>=5.1.2
+tabulate
 
 # Install tip of maestrowf
 -e git+https://github.com/LLNL/maestrowf.git#egg=maestrowf

workflows/feature_demo/feature_demo.yaml

@@ -12,11 +12,12 @@ env:
         WORKER_NAME: demo_worker
         VERIFY_QUEUE: default_verify_queue
 
-        HELLO: $(SPECROOT)/hello_world.py
-        FEATURES: $(SPECROOT)/features.json
-        TRANSLATE: $(SPECROOT)/translator.py
-        COLLECT: $(SPECROOT)/collector.py
-        MAKE_SAMPLES: $(SPECROOT)/make_samples.py
+        SCRIPTS: $(SPECROOT)/scripts
+        HELLO: $(SCRIPTS)/hello_world.py
+        FEATURES: $(SCRIPTS)/features.json
+        TRANSLATE: $(SCRIPTS)/translator.py
+        COLLECT: $(SCRIPTS)/collector.py
+        MAKE_SAMPLES: $(SCRIPTS)/make_samples.py
 
         SHARED: $(SPECROOT)/../shared
         LEARN: $(SHARED)/learn.py
@@ -137,7 +138,7 @@ merlin:
                 args: -l INFO --concurrency 3 --prefetch-multiplier 1 -Ofair
     samples:
         generate:
-            cmd: python $(SPECROOT)/make_samples.py -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy
+            cmd: python $(MAKE_SAMPLES) -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy
         # can be a file glob of numpy sample files.
         file: $(MERLIN_INFO)/samples.npy
         column_labels: [X0, X1]

workflows/feature_demo/requirements.txt

@@ -0,0 +1 @@
+sklearn

workflows/flux/flux_par.yaml

@@ -16,7 +16,7 @@ study:
 - description: Build the code
   name: build
   run:
-    cmd: mpicc -o mpi_hello $(SPECROOT)/hello.c >& build.out
+    cmd: mpicc -o mpi_hello $(SPECROOT)/scripts/hello.c >& build.out
     task_queue: flux_par
 - description: Echo the params
   name: runs 
@@ -60,4 +60,4 @@ merlin:
     column_labels: [V1, V2]
     file: $(MERLIN_INFO)/samples.npy
     generate:
-      cmd: python $(SPECROOT)/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 
+      cmd: python $(SPECROOT)/scripts/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 

workflows/flux/paper.yaml

@@ -19,7 +19,7 @@ study:
   name: build
   run:
     cmd: |
-      mpicc -o mpi_hello_sleep $(SPECROOT)/hello_sleep.c >& build.out
+      mpicc -o mpi_hello_sleep $(SPECROOT)/scripts/hello_sleep.c >& build.out
       # Add start time to flux
       flux wreck setenv FLUX_START_TIME=${FLUX_START_TIME}
       flux wreck setenv FLUX_START_SECONDS=${FLUX_START_SECONDS}
@@ -47,7 +47,7 @@ study:
   run:
     cmd: |
       #export PATH=/collab/usr/gapps/merlin/spack/idesign/${SYS_TYPE}/bin:$PATH
-      $(SPECROOT)/flux_info.py >flux_timings.out
+      $(SPECROOT)/scripts/flux_info.py >flux_timings.out
     depends: [runs*]
     task_queue: flux_paper
 
@@ -68,4 +68,4 @@ merlin:
     column_labels: [V1, V2]
     file: $(MERLIN_INFO)/samples.npy
     generate:
-      cmd: python $(SPECROOT)/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 
+      cmd: python $(SPECROOT)/scripts/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 

workflows/flux/requirements.txt

@@ -0,0 +1 @@
+

workflows/slurm/requirements.txt

@@ -0,0 +1 @@
+

workflows/slurm/slurm_par.yaml

@@ -13,7 +13,7 @@ study:
 - description: Build the code
   name: build
   run:
-    cmd: mpicc -o mpi_hello $(SPECROOT)/hello.c >& build.out
+    cmd: mpicc -o mpi_hello $(SPECROOT)/scripts/hello.c >& build.out
     task_queue: slurm_par
 - description: Echo the params
   name: runs 
@@ -46,4 +46,4 @@ merlin:
     column_labels: [V1, V2]
     file: $(MERLIN_INFO)/samples.npy
     generate:
-      cmd: python $(SPECROOT)/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 
+      cmd: python $(SPECROOT)/scripts/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 

workflows/slurm/slurm_test.yaml

@@ -40,4 +40,4 @@ merlin:
     column_labels: [V1, V2]
     file: $(MERLIN_INFO)/samples.npy
     generate:
-      cmd: python $(SPECROOT)/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy 
+      cmd: python $(SPECROOT)/scripts/make_samples.py -dims 2 -n $(N_SAMPLES) -outfile=$(MERLIN_INFO)/samples.npy