🐛 Fix --version, add enter, parse-resources and version, and …

…fix tests (#29)

.github/workflows/test_cpac.yml

@@ -19,10 +19,10 @@ jobs:
 
     strategy:
       matrix:
-        platform: [docker, singularity]
-        tag: [latest, dev-v1.8]
+        platform: [docker]
+        tag: [latest, nightly]
         go: [1.14]
-        python: [3.6, 3.7, 3.8]
+        python: [3.7, 3.8, 3.9, "3.10"]
         singularity: [3.6.4]
 
     steps:
@@ -39,45 +39,44 @@ jobs:
       run: python -m pip install --upgrade pip setuptools wheel
     - name: Set up Singularity
       if: ${{ matrix.platform == 'singularity' }}
-      uses: eWaterCycle/setup-singularity@v5
+      uses: eWaterCycle/setup-singularity@v7
       with:
         singularity-version: ${{ matrix.singularity }}
     - name: Prepare Singularity cache and tmp directories
       if: ${{ matrix.platform == 'singularity' }}
       run: mkdir -p ${SINGULARITY_CACHEDIR} && mkdir -p ${SINGULARITY_TMPDIR}
     - name: Install dependencies
       run: |
-        sudo apt-get install libarchive-dev \
-        libffi-dev \
-        flawfinder \
-        libgpgme11-dev \
-        libseccomp-dev \
-        squashfs-tools \
-        libssl1.1 libssl-dev \
-        libuuid1 uuid-dev
+        sudo apt-get install libffi-dev \
+                             flawfinder \
+                             libgpgme11-dev \
+                             libseccomp-dev \
+                             squashfs-tools \
+                             libssl1.1 libssl-dev \
+                             libuuid1 uuid-dev
         pip install -r requirements.txt
         pip install -r requirements-dev.txt
         pip install coverage coveralls nipype
     - name: Install cpac
       run: cd $GITHUB_WORKSPACE && pip install -e .
     - name: Test cpac, platform and tag specified
       run: |
-        coverage run --append -m pytest --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
+        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
         coverage report -m
     - name: Test cpac, platform specified, tag unspecified
       if: ${{ matrix.tag == 'latest' }}
       run: |
-        coverage run --append -m pytest --doctest-modules --platform ${{ matrix.platform }} .
+        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} .
         coverage report -m
     - name: Test cpac, platform unspecified, tag specified
       if: ${{ matrix.platform == 'docker' }}
       run: |
-        coverage run --append -m pytest --doctest-modules --tag ${{ matrix.tag }} .
+        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --tag ${{ matrix.tag }} .
         coverage report -m
     - name: Test cpac, platform and tag unspecified
       if: ${{ matrix.platform == 'docker' }} && ${{ matrix.tag }} == 'latest'
       run: |
-        coverage run --append -m pytest --doctest-modules .
+        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules .
         coverage report -m
     - name: Report coverage
       uses: AndreMiras/coveralls-python-action@v20201129
@@ -102,6 +101,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
     - name: Install cpac
       run: cd $GITHUB_WORKSPACE && pip install .
     - name: Configure Git credentials

.gitignore

@@ -12,6 +12,7 @@ __pycache__/*
 .cache/*
 .*.swp
 */.ipynb_checkpoints/*
+tmp
 
 # Project files
 .ropeproject
@@ -49,4 +50,5 @@ MANIFEST
 .venv*/
 
 # Singularity Images
-**/*.simg
+**/*.simg
+**/*.sif

CHANGELOG.rst

@@ -3,7 +3,14 @@ Changelog
 =========
 `Unreleased`
 ================================================================================================
-* 🧮 Evaluates memory usage for specific nodes from `callback.log` files
+* 🧮 Evaluates memory usage for specific nodes from ``callback.log`` files
+* ✨ Adds ``enter`` command to enter a container's ``BASH``
+* ✨ Adds ``version`` command to give version of in-container C-PAC
+* 🐛 Fixes issue where ``--version`` command was not working
+* 🐛 Fixes issue where custom pipeline configurations were not binding to temporary container prior to checking for bind paths
+* ✅ Updates for tests that were failing
+* 📝 Add known issues to usage string
+* ⬆ Require Python ≥ 3.7 (for typing annotations)
 
 `Version 0.4.0: Goodbye Singularity Hub <https://github.com/FCP-INDI/cpac/releases/tag/v0.4.0>`_
 ================================================================================================

README.rst

@@ -14,12 +14,12 @@ C-PAC Python Package is a lightweight Python package that handles interfacing a
 Dependencies
 ============
 
-* `Python <https://www.python.org>`_ ≥3.6
+* `Python <https://www.python.org>`_ ≥3.7
 * `pip <https://pip.pypa.io>`_
 * At least one of:
 
   * `Docker <https://www.docker.com>`_
-  * `Singularity <https://sylabs.io/singularity>`_ ≥2.5&≤3.0
+  * `Singularity <https://sylabs.io/singularity>`_ ≥2.5
 
 Usage
 =====
@@ -32,7 +32,8 @@ Usage
     usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
                 [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
                 [--working_dir PATH] [-v] [-vv]
-                {run,group,utils,pull,upgrade,crash} ...
+                {run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
+                ...
     
     cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images. 
     
@@ -57,8 +58,40 @@ Usage
     
     	cpac run --help
     
+    Known issues:
+    - Some Docker containers unexpectedly persist after cpac finishes. To clear them, run
+        1. `docker ps` to list the containers
+      For each C-PAC conatainer that persists, run
+        2. `docker attach <container_name>`
+        3. `exit`
+    - https://github.com/FCP-INDI/cpac/issues
+    
     positional arguments:
-      {run,group,utils,pull,upgrade,crash}
+      {run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
+        run                 Run C-PAC. See
+                            "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] run --help"
+                            for more information.
+        utils               Run C-PAC commandline utilities. See
+                            "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] utils --help"
+                            for more information.
+        version             Print the version of C-PAC that cpac is using.
+        group               Run a group level analysis in C-PAC. See
+                            "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] group --help"
+                            for more information.
+        pull (upgrade)      Upgrade your local C-PAC version to the latest version
+                            by pulling from Docker Hub or other repository.
+                            Use with "--image" and/or "--tag" to specify an image
+                            other than the default "fcpindi/c-pac:latest" to pull.
+        enter (bash, shell)
+                            Enter a new C-PAC container via BASH.
+        parse-resources (parse_resources)
+                            When provided with a `callback.log` file, this utility can sort through
+                            the memory `runtime` usage, `estimate`, and associated `efficiency`, to
+                            identify the `n` tasks with the `highest` or `lowest` of each of these
+                            categories.
+                            "parse-resources" is intended to be run outside a C-PAC container.
+                            See "cpac parse-resources --help" for more information.
+        crash               Convert a crash pickle to plain text (C-PAC < 1.8.0).
     
     optional arguments:
       -h, --help            show this help message and exit

requirements.txt

@@ -1,4 +1,5 @@
 docker >= 4.2.1
+dockerpty
 docker-pycreds
 pandas >= 0.23.4
 pyyaml

setup.cfg

@@ -23,7 +23,7 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Topic :: Scientific/Engineering :: Bio-Informatics
-version = 0.4.1
+version = 0.5.0
 
 [options]
 zip_safe = False
@@ -37,14 +37,16 @@ setup_requires =
     pyyaml
 install_requires =
     docker
+    dockerpty
     docker-pycreds
     pandas >= 0.23.4
     spython >= 0.0.81
     pyyaml
+    rich
     tabulate >= 0.8.6
     tornado
     websocket-client
-python_requires = >=3.6
+python_requires = >=3.7
 
 [options.packages.find]
 where = src