Added SLURM and Conda support

- Modified exe function in base_script.sh.template to support
  aliases
- Added `conda install` support in base_script.sh.template
- Added SLURM support with slurm-script.sh.template
- SLURM support wraps given commands with SLURM commands using bash
  aliases
- Added usage instructions for slurm-script.sh.template and
  remote.sh.template
- Updated secret.tar.enc to use abrghost instead of abrgl

.nengobones.yml

@@ -22,6 +22,7 @@ travis_yml:
       test_args: --test-arg --test-arg
     - script: remote
     - script: remote-test
+    - script: remote-slurm-test
     - script: test-coverage
       env:
         TEST_LOCAL_VAR: test local var val
@@ -98,7 +99,7 @@ ci_scripts:
     pre_commands:
       - cat .ci/remote.sh
     travis_var_key: 2895d60e3414
-    host: gl
+    host: abrghost
   - template: test
     pre_commands:
       - cat .ci/test-for-remote.sh
@@ -110,7 +111,24 @@ ci_scripts:
     remote_script: test-for-remote
     output_name: remote-test
     travis_var_key: 2895d60e3414
-    host: gl
+    host: abrghost
+    coverage: true
+  - template: remote-script
+    pre_commands:
+      - cat .ci/remote-slurm-test.sh
+    remote_script: test-for-slurm
+    output_name: remote-slurm-test
+    travis_var_key: 2895d60e3414
+    host: abrghost
+    coverage: true
+  - template: slurm-script
+    pre_commands:
+      - cat .ci/test-for-slurm.sh
+    slurm_command: "srun -pCI"
+    wrapped_commands:
+      - pytest
+    slurm_script: test-for-remote
+    output_name: test-for-slurm
     coverage: true
   - template: docs
     pre_commands:

.travis.yml

@@ -53,6 +53,9 @@ jobs:
   -
     env:
       SCRIPT="remote-test"
+  -
+    env:
+      SCRIPT="remote-slurm-test"
   -
     env:
       TEST_LOCAL_VAR="test local var val"

CHANGES.rst

@@ -45,6 +45,8 @@ Release History
 - Added support for changing the main branch name with the ``main_branch``
   config option. (`#145`_)
 - Added template for ``version.py``. (`#151`_)
+- Added support for ``conda install`` in CI scripts (`#152`)
+- Added template for running CI scripts through SLURM on remote machines (`#152`)
 
 **Changed**
 
@@ -92,6 +94,7 @@ Release History
 .. _#144: https://github.com/nengo/nengo-bones/pull/144
 .. _#145: https://github.com/nengo/nengo-bones/pull/145
 .. _#151: https://github.com/nengo/nengo-bones/pull/151
+.. _#152: https://github.com/nengo/nengo-bones/pull/152
 
 0.11.1 (April 13, 2020)
 =======================

nengo_bones/config.py

@@ -249,6 +249,8 @@ def validate_ci_config(ci_config):
         "pre_commands",
         "post_commands",
         "codespell_ignore_words",
+        "conda_install",
+        "wrapped_commands",
     )
     for opt in list_opts:
         check_list(ci_config, opt)

nengo_bones/templates/base_script.sh.template

@@ -14,7 +14,7 @@ exe() {
     for i in "${!args[@]}"; do
       [ -n "${args[$i]}" ] || unset "args[$i]"
     done
-    "${args[@]}" || { echo -e "\033[1;31mCOMMAND '${args[0]}' FAILED\033[0m"; STATUS=1; }
+    eval '"${args[@]}"' || { echo -e "\033[1;31mCOMMAND '${args[0]}' FAILED\033[0m"; STATUS=1; }
 }
 
 if [[ ! -e {{ pkg_name }} ]]; then
@@ -25,12 +25,16 @@ fi
 
 if [[ "$COMMAND" == "install" ]]; then
     {% block install %}
+    {% if conda_install %}
+    exe conda install {%- for pkg in conda_install %} "{{ pkg }}" {%- endfor %}
+
+    {% endif %}
     {% if pip_install %}
     exe pip install {%- for pkg in pip_install %} "{{ pkg }}" {%- endfor %}
 
-    {% else %}
+    {% endif %}
+    {% if not conda_install and not pip_install %}
     :
-
     {% endif %}
     {% endblock %}
 elif [[ "$COMMAND" == "before_script" ]]; then

nengo_bones/templates/remote.sh.template

@@ -53,6 +53,24 @@ and logged in with `travis login --com`
 
 See https://docs.travis-ci.com/user/encrypting-files/ for more details.
 
+
+Usage Instructions
+==================
+
+This script executes a NengoBones generated CI script on a remote machine.
+
+.nengobones.yml parameters:
+
+`host`: The <hostname> of the remote machine defined in the `config` file above.
+
+`travis_var_key`: The TravisCI variable key as defined in Step 6 of the setup
+instructions above.
+
+`remote_script`: The name of the script to be executed on the remote machine. This
+script must be defined as a separate entry in the `ci_scripts` section of yml file.
+
+`output_name`: Desired output name of the generated CI script.
+
 #}
 
 {% set pkg = pkg_name | replace("_", "-") %}

nengo_bones/templates/slurm-script.sh.template

@@ -0,0 +1,76 @@
+{% extends "templates/base_script.sh.template" %}
+
+{#
+
+Usage Instructions
+==================
+
+This script is intended to be used to apply a SLURM wrapper around other NengoBones
+generated CI scripts.
+
+.nengobones.yml parameters:
+
+`slurm_command`: The SLURM command used to create the SLURM job. Use quotations to avoid
+problems with the space character. Examples:
+    - "srun"
+    - "srun -pCI -G1"
+    - "sbatch"
+
+`wrapped_commands`: A list of commands to be wrapped with `slurm_command`. The command
+will be executed as: <slurm_command> <command>
+Example, if <slurm_command> is "srun -pCI", and <command> is "pytest", then the command
+will be executed as "srun -pCI pytest"
+
+`slurm_script`: The CI script to be executed, but using the SLURM-wrapped commands
+instead of the typical non-SLURM invocation.
+
+`output_name`: Desired output name of the generated CI script.
+
+#}
+
+{% block install %}
+    bash .ci/{{ slurm_script }}.sh install || STATUS=1
+{% endblock %}
+
+{% block before_script %}
+    bash .ci/{{ slurm_script }}.sh before_script || STATUS=1
+{% endblock %}
+
+{% block script %}
+    # Enable `expand_aliases` option for bash interpreter
+    shopt -s expand_aliases
+
+    # Create aliases for commands to include SLURM command prefix
+    {% for command in wrapped_commands %}
+    alias {{ command }}="{{ slurm_command }} {{ command }}"
+    echo "Created alias for {{ command }}: "
+    type -a {{ command }}
+
+    {% endfor %}
+    # Run script. Use existing shell instead of subshell to ensure alias applies.
+    . .ci/{{ slurm_script }}.sh script || STATUS=1
+{% endblock %}
+
+{% block before_cache %}
+    bash .ci/{{ slurm_script }}.sh before_cache || STATUS=1
+{% endblock %}
+
+{% block after_success %}
+    bash .ci/{{ slurm_script }}.sh after_success || STATUS=1
+{% endblock %}
+
+{% block after_failure %}
+    bash .ci/{{ slurm_script }}.sh after_failure || STATUS=1
+{% endblock %}
+
+{% block before_deploy %}
+    bash .ci/{{ slurm_script }}.sh before_deploy || STATUS=1
+{% endblock %}
+
+{% block after_deploy %}
+    bash .ci/{{ slurm_script }}.sh after_deploy || STATUS=1
+{% endblock %}
+
+{% block after_script %}
+    bash .ci/{{ slurm_script }}.sh after_script || STATUS=1
+{% endblock %}

nengo_bones/tests/test_config.py

@@ -70,6 +70,18 @@ def test_validate_config():
         config.validate_config(init_cfg)
     test_cfg["pre_commands"] = ["command"]
 
+    # error when conda_install is a string instead of list
+    test_cfg["conda_install"] = "conda_req"
+    with pytest.raises(TypeError, match="conda_install should be a list"):
+        config.validate_config(init_cfg)
+    test_cfg["conda_install"] = ["conda_req"]
+
+    # error when wrapped_commands is a string instead of list
+    test_cfg["wrapped_commands"] = "command"
+    with pytest.raises(TypeError, match="wrapped_commands should be a list"):
+        config.validate_config(init_cfg)
+    test_cfg["wrapped_commands"] = ["command"]
+
     # error when only one of pre_commit_config_yaml or pyproject_toml exists
     init_cfg["pyproject_toml"] = {}
     with pytest.raises(KeyError, match="must define both"):