Merge pull request #2 from LLNL/master

merge master

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,47 @@
+# Merlin Community Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the Merlin project or its community. Examples of representing the project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of the project may be further defined and clarified by Merlin maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,35 @@
+---
+name: Bug report
+about: Create a report to help Merlin improve
+title: "[BUG]"
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Please answer these questions to help us pinpoint the problem**
+- Does the problem occur in `merlin run --local` mode, distributed mode or neither?
+- If a distributed problem, which backend and queue servers are you using? How are they configured?
+- On what machines/architectures are you running merlin? Is this bug on a specific machine or can you reproduce it elsewhere?
+
+**Please run `merlin info` and paste the results here:**
+
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for Merlin
+title: "[FEATURE]"
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.travis.yml

@@ -0,0 +1,24 @@
+language: python
+python: 
+  - "3.6"
+  - "3.7"
+  - "3.8"
+install: 
+  - "pip install --upgrade pip"
+  - "pip install cryptography"
+  - "pip install -r requirements.txt"
+  - "pip install -e ."
+  - "pip install -r requirements/mysql.txt"
+  - "pip install --upgrade sphinx"
+script: 
+  - "merlin config"
+  - "python -m pytest tests/"
+  - "python tests/integration/run_tests.py --verbose --ids 1 2 3 4 5 6 7 8 9 12 13 18 19 20"
+deploy:
+  provider: pypi
+  user: "__token__"
+  password:
+    secure: Bd4xw0sEPixUiOwnl+5MYQaSX8SHKc0Dughg2Ls/B/e3NcvmCbYeBEz+2yclByffdNkxrQCTzMI90gZ5i7aKBuzEZ4E/RHXytwoLWOIKw3rE5jun44Vb9anLz2V+hEF6DSZ47fe+5re0D/TKCjtP7KTqLTDDdgg6+f648IbiE2CCmJXXeia48MzkUlLHYRbIuyWXGhaQasZwIoZQ872+xX0n8/3p+bV6BZ415DwJSsEdFmDu/F9drSVLUV6monU4eIfVoveos4HPH76J5WDMlwq6ZMaxF5E88ExiM9JJ4KNrrxBgLFS2I0BZmI92edHqtSs6TWz7Qo4wvW/6emosQjs6EWS8JmhSMdMFyhBos+Mx6HJYqJb4Nxcx9vclcpWSSzKSKUkAKX7bN5+v2Oy5BXfCdLBxWY+et+6ZY7/SzutOfgPmEz7BG7YiC9vZAGYpas4H3C6sOAdIb8y2lvL9Vht1+94GITZ0nFzdmpNGmAN6g9BAPvrEVWnZKdy0qpcBIpS/KW0N5/8jG74D0ouEDRgH5ahV5+RoyzzGrShC2XBHne4bGHb59DHWBRJBo2bS2Df0+gZPsd15kfjOCyZNHUIni2yQ83GgGc7hznLJd/UIvvPTGG42LjppzER5kimGor8BZ3B58dKrHqqFgRyAowOgoVlhd01rMi4a1QwS6ao=
+  on:
+    tags: true
+    branch: master

CONTRIBUTING.md

@@ -0,0 +1,15 @@
+# Contributing
+
+Merlin is open source software, and we welcome contribution!
+
+We follow a gitflow - like [this](http://www.dalescott.net/using-gitflow-with-githubs-fork-pull-model/).
+To contribute, fork your own copy.
+All changes are done via pull requests from your fork into the appropriate main repository branch.
+Features and additions into `develop`, hot fixes into `master`.
+
+### Squash
+Before merging a pull request, please [squash your commits](https://github.com/LLNL/merlin/wiki/Squash-commits) down to a single concise commit message.
+
+### More...
+Complete developer documentation is [here](https://merlin.readthedocs.io/en/latest/merlin_developer.html).
+

README.md

@@ -1,16 +1,6 @@
-<img src="docs/images/merlin.png" width="400"
-alt="
-           *      
-       *~~~~~                                       
-      *~~*~~~*      __  __           _ _       
-     /   ~~~~~     |  \/  |         | (_)      
-         ~~~~~     | \  / | ___ _ __| |_ _ __  
-        ~~~~~*     | |\/| |/ _ \ '__| | | '_ \ 
-       *~~~~~~~    | |  | |  __/ |  | | | | | |
-      ~~~~~~~~~~   |_|  |_|\___|_|  |_|_|_| |_|
-     *~~~~~~~~~~~                                    
-       ~~~*~~~*    Machine Learning for HPC Workflows                                 
-">
+![alt text][logo]
+
+[logo]: https://github.com/LLNL/merlin/blob/master/docs/images/merlin.png "Merlin logo"
 
 Welcome to the Merlin README, a condensed guide. For more in-depth Merlin
  information, try our [web docs here](https://merlin.readthedocs.io/).
@@ -121,6 +111,10 @@ namely a demo workflow that has simulation and machine-learning:
 More documentation on the example workflows can be found under
 'Running the Examples'.
 
+# Code of Conduct
+Please note that Merlin has a
+[**Code of Conduct**](.github/CODE_OF_CONDUCT.md). By participating in
+the Merlin community, you agree to abide by its rules.
 
 # Running the Examples
 Example workflows can be found in the `workflows/` directory.

docs/source/spack.rst

@@ -9,16 +9,6 @@ Merlin will then be installed in this specific version allowing for
 multiple python versions on a single system without the need for a
 virtualenv. The py-merlinwf package builds with python3.6+.
 
-Checkout merlin spack repo
-**************************
-
-
-Get the latest version of merlin.spack from github.
-
-::
-
-  git clone https://github.com/LLNL/merlin.spack.git
-
 
 Checkout spack
 **************
@@ -32,6 +22,16 @@ make sure merlin and spack are in separate directories.
   git clone https://github.com/spack/spack.git
 
 
+The merlin addition to spack is currently in pull requests, you can clone a 
+branch that has all of the PR changes here:
+
+.. code:: bash
+
+  git clone https://github.com/koning/spack.git
+  cd spack
+  git checkout feature/koning/merlinwf
+
+
 Setup spack
 ***********
 
@@ -57,18 +57,12 @@ To see the compilers.
 
     spack compiler list
 
-Add the merlin.spack repo to spack (done once):
-
-.. code:: bash
-
-    spack repo add <path>/<to>/merlin.spack
-
 
 Build merlin
 ************
 
-Build merlin, this will take a *long* time, be prepared to wait.  It is going
-to build python and everything python needs including numpy.
+Build merlin, this will take a *long* time, be prepared to wait.  It will
+build python and all python modules merlin needs including numpy.
 
 .. code:: bash
 

merlin/__init__.py

@@ -37,7 +37,8 @@
 import os
 import sys
 
-__version__ = "1.0.0"
+
+__version__ = "1.0.2"
 VERSION = __version__
 PATH_TO_PROJ = os.path.join(os.path.dirname(__file__), "")
 

merlin/celery.py

@@ -29,10 +29,7 @@
 ###############################################################################
 
 """Updated celery configuration."""
-from __future__ import (
-    absolute_import,
-    print_function,
-)
+from __future__ import absolute_import, print_function
 
 import logging
 import os
@@ -43,10 +40,7 @@
 from celery.signals import worker_process_init
 
 import merlin.common.security.encrypt_backend_traffic
-from merlin.config import (
-    broker,
-    results_backend,
-)
+from merlin.config import broker, results_backend
 from merlin.log_formatter import FORMATS
 from merlin.router import route_for_task
 

merlin/common/sample_index_factory.py

@@ -33,10 +33,7 @@
 """
 from parse import parse
 
-from merlin.common.sample_index import (
-    MAX_SAMPLE,
-    SampleIndex,
-)
+from merlin.common.sample_index import MAX_SAMPLE, SampleIndex
 from merlin.utils import cd
 
 

merlin/common/tasks.py

@@ -29,34 +29,18 @@
 ###############################################################################
 
 """Test tasks."""
-from __future__ import (
-    absolute_import,
-    unicode_literals,
-)
+from __future__ import absolute_import, unicode_literals
 
 import logging
 import os
 
-from celery import (
-    chain,
-    chord,
-    group,
-    shared_task,
-    signature,
-)
-from celery.exceptions import (
-    OperationalError,
-    TimeoutError,
-)
+from celery import chain, chord, group, shared_task, signature
+from celery.exceptions import OperationalError, TimeoutError
 
 from merlin.common.abstracts.enums import ReturnCode
 from merlin.common.sample_index import uniform_directories
 from merlin.common.sample_index_factory import create_hierarchy
-from merlin.exceptions import (
-    HardFailException,
-    InvalidChainException,
-    RetryException,
-)
+from merlin.exceptions import HardFailException, InvalidChainException, RetryException
 from merlin.router import stop_workers
 from merlin.spec.expansion import (
     parameter_substitutions_for_cmd,

merlin/display.py

@@ -37,10 +37,7 @@
 from tabulate import tabulate
 
 from merlin.ascii_art import banner_small
-from merlin.config import (
-    broker,
-    results_backend,
-)
+from merlin.config import broker, results_backend
 from merlin.config.configfile import default_config_info
 
 

merlin/main.py

@@ -42,16 +42,10 @@
 )
 from contextlib import suppress
 
-from merlin import (
-    VERSION,
-    router,
-)
+from merlin import VERSION, router
 from merlin.ascii_art import banner_small
 from merlin.log_formatter import setup_logging
-from merlin.spec.expansion import (
-    RESERVED,
-    get_spec_with_expansion,
-)
+from merlin.spec.expansion import RESERVED, get_spec_with_expansion
 from merlin.study.study import MerlinStudy
 from merlin.utils import ARRAY_FILE_FORMATS
 

merlin/spec/expansion.py

@@ -30,16 +30,10 @@
 
 import logging
 from collections import ChainMap
-from os.path import (
-    expanduser,
-    expandvars,
-)
+from os.path import expanduser, expandvars
 
 from merlin.common.abstracts.enums import ReturnCode
-from merlin.spec.override import (
-    dump_with_overrides,
-    error_override_vars,
-)
+from merlin.spec.override import dump_with_overrides, error_override_vars
 from merlin.spec.specification import MerlinSpec
 
 

merlin/study/celeryadapter.py

@@ -37,16 +37,8 @@
 import time
 from contextlib import suppress
 
-from merlin.study.batch import (
-    batch_check_parallel,
-    batch_worker_launch,
-)
-from merlin.utils import (
-    get_procs,
-    get_yaml_var,
-    is_running,
-    regex_list_filter,
-)
+from merlin.study.batch import batch_check_parallel, batch_worker_launch
+from merlin.utils import get_procs, get_yaml_var, is_running, regex_list_filter
 
 
 LOG = logging.getLogger(__name__)