This change log spiritually adheres to these guidelines.
Categories for each release: Added, Changed, Deprecated, Removed, Fixed, Security
No significant changes
- Remote builders for 16.04 v1, 20.04
- Asset builder for 20.04
- '--verbose' flag for
dx-mount-all-inputs
- Provide project-id in batch tsv file
- Archival api wrappers
- Hide
notebook
andloupe-viewier
fromdx
help output
- Macos tarball build
- Ubuntu 20.04 build targets
- jackson-databind from 2.9.10.3 to 2.9.10.5
- API wrapper generation with Python 3
dx-clone-asset
when no project exists- DXJava DXDataObject.Rename()
- Python cryptography version >= 2.3
dx-clone-asset
with Python 3
- Ubuntu 14.04 builds
- Examples for
dx find
with negative timestamp dx build --from applet-xxx
for app- --brief option to dx build for apps and applets
- Error handling during syntax check for dx build
- Python 2.7 example applets to use Python 3
- Commit dxpy version during release
dx get
for applets withpython3
interpreterdx-upload-all-outputs ---xattr-properties
parsing
- Python 2.7 example applets to use Python 3
- Commit dxpy version during release
- No significant changes
dx-mount-all-inputs
for dxfuse- Sci Linux compilation option for upload agent
- Python 3 interpreter for
dx-app-wizard
- dxR build
dx upload
retry for "SSL EOF" error- Error out for dx run --clone with analysis and executable
- runSpec.version dxapp.json key for 16.04 applets
dx build_asset
support for runSpecVersion key in dxasset.json
- Python documentation build
- dxpy tests in Python 3
- Bump jackson-databind from 2.9.10 to 2.9.10.1
- Bump jackson-databind from 2.9.10 to 2.9.10.1
- Retry symlink file downloads with
aria2c
- Python3 issue in dx app builder test
- Remote app tarball builder for xenial
- Allow disabling system exit on log client
- database class in dx find data
- Python3 compatibility for exec environment scripts
- pip3 package manager for execDepends
- Precise debian package build target
- Run job as high priority if '--ssh' provided
- Project deletion warning if specifying file-id
- New instance types to
dx-app-wizard
- Upgrade jackson to 2.9.10
- Python 3 wrapper generation and tests
dx get
for database files- v2 instance types in
dx-app-wizard
- Generating ruby wrappers in python 3
- dx-app-wizard in python 3
- Documentation links to https://documentation.dnanexus.com
- Remove non-ascii char from readme
- '--xattr-properties' argument for dx-upload-all-outputs to include fs metadata as k,v properties
- xattr dependency for Linux builds
- Only require futures package for python 2.7
- Upgrade build dependencies for pip, setuptools, and wheel
- DXJava support for proxies
- Approved tools CLI for
dx update project
- Upgrade jackson-databind and jackson-core to version 2.9.8
- Provide project ID for dx make_download_url unless in job workspace
- Enabling argcomplete for
dx
installed with debian package in worker environment
dx upgrade
downloads the latest version from s3
- Reduce the number of API calls for
dx download
dx upload
error via proxy in Azure
- support for passing HTTPContext in
DXJava
to theexecute()
operation
--instance-count
todx run
so that Spark cluster size can be defined at app start
dx wait
behavior by adding exponential backoff and passing appropriate project- Decreased libcurl timeout in C++ bindings from infinity to default 10 min
- Default Ubuntu release to 16.04 in
dx-app-wizard
- Link handling to better support JBORs
- Handling file arrays in batch job runner
- no significant updates
- new
findDataObjects
inputs to DXJava - project name resolution to
--project
flag fordx run
- smart reuse and SAML identity provider
dx list database <entity>
for DNAnexus Apollo--ignore-reuse
and--ignore-reuse-stage
working fordx run <workflow>
- Upgrade
proot
to be compatible with kernel >= 4.8 - Skip symlinks test in isolated environment
- Uploading binary data, such at compressed files, works in python3.
- python3 parsing subcommand help output
- Binary mode for opening dx:files.
- A
--unicode
flag for command line tools that need to handle unicode text files. For example:dx cat --unicode file-xxxx
. This was added forcat
, anddownload
.
- 32-bit build target for Ubuntu 14.04
gtable
code
--phi
flag fordx new project
- Bug in downloading symlinks when using aria2c
- Max number of aria2c connections <= 16
- argcomplete eval in the worker when sourcing
environment
- Preserve
httpsApp
field in dxapp.json when callingdx get
- The
--except [array:file variable]
option fordx-download-all-inputs
- upload issue using api proxy in Python 3
--no-project
option indx-jobutil-parse-link
- A script for reconnecting to a jupyter notebook session
- support for dx building a global workflow with apps in multiple regions
- Mark Ubuntu 12.04 as deprecated in
Readme
- setting instance types on global workflow stages
- fix test code for Spark 2.4.0 upgrade
- symlink download with
aria2
No significant changes
- Update MANIFEST.in to include python
Readme
- Writing to stdout for py2 in
dx cat
- Python virtualenv path in traceability runner
- Failing
build app
when suggestion is not a dxlink - Handle keyboard interrupt and system exit gracefully
- Use absolute path to set argcomplete
- If a bash variable is long, print a warning, do not omit it
- Issue with backports deps on Windows
- Make
dx-toolkit
python 2 and 3 compatible - Update macOS gnureadline version
- Allow Windows to use certifi CA bundle
- Update bindings for Apollo API routes
- Update urllib import in
dx-docker
- Update requests in
make doc
target
- Test that attempts to upload to a closed file
- First draft of an environment file for fish shell
- If available, use
aria2
rather thanwget
as it's much faster
- Use of ubuntu 12.04 in
test_dxclient.py
- Old asset building script
- Rare subcommands (
compile
,compile_dxni
,sh
) - The
dx-run-app-locally
script
jackson-databind
andjackson-core
upgrade
- Update cran repository
- Add release/distro to example app
dxapp.json
files
- Download links for
docker2aci
- The test error: No root certificates specified for verification of other-side certificates
- A convenience login script for a cloud workstation
- Add
parents
param toclone()
- Allow batch IDs as output folders for batch run
- Setting a handler for a global workflow
- Redirecting proxy printout to stderr
cat
argument too long in a bash script- Ensure we can pop items from the main dictionary (python3)
- Warn user before
dx rm -r
on root of a project - Let
urllib3
set default CA bundle on Windows - Updgrade
pyopenssl
for test suite to 17.5.0 - Replace
ws4py
with websocket-client library injob_log_client
- Pass stages input from assetDepends to bundledDepends
- Traceability ID for locked workflow test (#406)
- Python 3 incompatibilites
- Python 3
dx upload
import dxpy
whensys.stdin
isNone
dxpy.describe()
used with a list of object IDs and an additionalfields
argument
- Sort inputs in
dx generate_batch_inputs
- 12.04 builds
- Windows install Python version upgrade to 2.7.15
- Windows installation
dx run --ignore-reuse
to disable job reuse for jobignoreReuse
key in dxapp.json
- dxWDL version 0.74
- Ubuntu release and asset version as parameters for
dx-docker create-asset
- Builds for Ubuntu 16.04
dx wait
where a file with object IDs is provided in pathdx compile
for debian install dxWDL.jar filepath
- Database wrappers
- Support dxni compilation
- requests >= 2.8.0
- psutil >= 3.3.0
- Python 3 incompatibilities
- Revert of finding project for data object
- support for setting and updating
details
on global workflows - decorators for traceability tests
dx watch
support for smart reuse- test for
dx watch
job log relay dx find jobs/executions
support for smart reuse- ability to provide a file which contains a list of jobs or data objects upon which to
dx wait
dxWDL
integration (dx compile
command)
python-dateutil
version upgrade to 2.5
- unclear behavior when
--clone
,--folder
, and--project
are simultaneously provided todx run
DXObject.set_ids()
with project set to None (it is now set to an arbitrary project associated with the file)- bash helpers tests
- Cosmetic update to
dx publish
dx publish
now sets thedefault
alias on the published version by default
- Support for updating a global workflow
- Wiki links to API documentation for API wrappers
- addTags/removeTags API wrappers for global workflow
- Better checking for inputs and/or inputSpec before batch running workflows
- A workflow must be closed before initializing a global workflow from it (test updates for API changes)
- Remove the "temporary" field from
dx describe workflow-xxxx
- "Deleted" field to
dx describe globalworkflow-xxxx
- a note to
dx describe
that the workflow is locked
- Print proper dx describe analysis of a global workflow
dx publish
command- inline cluster bootstrap script
- dx run for global workflows
- dx find apps tests
- resolve paths for global workflows
- add, remove, list users for global workflows
- add, remove, list developers for global workflows
- public project test
- API tests
- Support for dx find global workflows
- Initial support for dx build global workflow
- Publish method to global workflow bindings
- Support for dx get global workflow
dx download
for symlinks
- Support for
dx describe
for global workflows
- zsh support
- API wrappers for global workflow routes
- Basic Python bindings for global workflow
set_properties()
method to DXProject
- dx get applet without execDepends
dx-clone-asset
SSL error
- Clarify documentation of stage key for
dx run
- Asset builder support for Ubuntu 16.04
--singlethread
parameter fordx upload
dx-docker pull
retries more often
- c-ares package version for upload agent build
- Bug with Azure instance type selection in
dx-app-wizard
- Do not retry code
422
in dxpy
socketTimeout
andconnectionTimeout
parameters to JAVADXEnvironment
(thanks, @pkokoshnikov)- Generate batch inputs CLI
- Accept 302 as a success for
ua --test
- Batch runner CLI
- Updated c-ares and file packages (related to upload agent builds)
- API wrappers for
[applet,app,workflow]-xxxx/validateBatch
- Issue where dx-clone-asset doesn't create projects in different regions if they don't already exist
- App version and published/unpublished note to
dx run -h <app>
- Recursive search for asset in a path is disabled, and we strictly enforce only one matching asset name
- Use twine for pypy uploads
- Error that blocks org from being added as developers
dx-docker
: cleanup of the quote code (regression fix)dx-docker
: useshutil.move()
instead ofos.rename()
with the aci image- Accept 'http_proxy', 'HTTP_PROXY', 'https_proxy', 'HTTPS_PROXY' for proxy environmental variables
- Error out instead of warning when old pricing scheme is used in
dxapp.json
- Fix certain tests flakiness
- Warning when
runSpec.release
is not specified indxapp.json
with a note it will be required in the future - Numerous enhancements to Jupyter notebook support (see https://github.com/dnanexus/dx-toolkit/commit/7ecbcb6b75118c0acd27f7a7cfe37d0a19e6d6c3 for more information)
dx-app-wizard
anddx get
specify systemRequirements inregionalOptions
and not inrunSpec
ofdxapp.json
- multiple updates to jupyter notebook support
- setting
systemRequirements
inrunSpec
ofdxapp.json
dx-configset-to-fasta
script
dx-clone-asset
sets the default regions to be all regions that user has access to and skips redundant cloning to current regiondx build
now works seamlessly across apps and applets
- Update run input help and describe messages for locked workflows
- Warn when old, top-level pricing policy scheme is used in dxapp.json
dx-gtable-to-csv
anddx-gtable-to-tsv
scriptsdx-workflow-to-applet
scriptinclude_hidden_links
parameter from clone()
- dx-toolkit and apt conflict with argcomplete
- dx-clone-asset script
dx-docker
: ignore user argument if given- TLS documentation
- app building tests now include
runSpec.release
andrunSpec.distribution
in app specs dx-docker
: better handling of quotes
- New InvalidTLSProtocol Exception raised when connection fails due to wrong TLS protocol.
- Remove rstudio option for
dx notebook
- dx-toolkit and apt conflict with jq
- Azure instance types to the list of available types in
dx-app-wizard
- ua -- test now displays system messages coming from the apiserver.
- Update references to workflow
inputs
andoutputs
to keep them in sync with API changes
- No significant changes
- Priority arg to
build_asset
- Pass region-specific pricing policy in dxapp.json
- Execution of old workflows built without explicit IO
- CLI support for workflow lockdown
- Deprecated
dx-mount
- Initial 'dx notebook' commit
- Python bindings for workflow-level input and output
- Support for the 'downloadRestricted' flag
- Default to 14.04 release for all instance types in
dx-app-wizard
- No significant changes
- Point release to fix release version issues
- dx-jobutil-new-job now properly supports instance type
- Installation instructions now centralized on Github page
- Incrementally upgraded dependencies for Java bindings
- Helper script to check TLS 1.2 support
- A
region
parameter can now be passed todx find projects
,dx find data
,dx find org projects
- No significant changes
- A
region
parameter can now be passed todxpy.find_data_objects()
anddxpy.find_projects()
dx-docker
now no longer bind mounts$HOME
and/tmp
into the guest as this is consistent with Docker
- Python 3 compatibility with
dx-app-wizard
dx get
does not redundantly inline description and developerNotes in dxapp.json any more
- Client support for partial folder deletion
- Add methods
__next__()
andnext()
to DXFile to complete iteration interface (thanks to Eric Talevich!)
--bill-to
option is utilized when building multi-region apps withdx build
- Mac install no longer uses virtualenv. Instead, we ask users to install desired version of Python
- dx-docker bug where environment variables passed in through the CLI do not get set within container
dx build
creates a workflow on the platform based on the workflow's local source directory
- the deprecated
dx-build-app
anddx-build-applet
scripts (that were replaced withdx build
) were removed
- Bug introduced in release 204.0: including app resources fails
- Ability to specify additional resources for multi-region apps
dx ls -l
and friends now request only needed describe fields
- Ability to specify bundledDepends and assetDepends for multi-region apps
- Use DNAnexus DockerHub repo for dx-docker tests
- Issue where selecting from exactly 10 projects resulted in a stacktrace error
dx get workflow-xxxx
creates a local representation of a workflow
No significant changes.
- Python 3 compatibility with
repr
import
No significant changes.
- dx-docker test suite to toolkit
- Retry download of Docker image if there is transient network failure
- Allow image ID as a parameter for
dx-docker
; see wiki documentation for more details
- missing pyasn1 module for OSX list of install dependencies; gets rid of import warning messages
- Alternative export for
dx-docker
when docker image is improperly exported by docker engine
dx run -i=filename
now prompts user to select input file if duplicate filenames exist in projectdx-docker create-asset
now supports output pathdx download
failure when run within project that user has lost access todx build -f
now removes all applets with matching name/directory
dx-docker run
KeyError when docker image is built from container
- Recursive file upload on Windows for the Upload Agent
- Show download progress for calls to
dx download -r
- Issue where calls to
dxpy.download_all_inputs(parallel=True)
hang
- Upload agent now does not gzip compress .gz files on Ubuntu 14.04
- Minor log message fix if file is already uploaded
- Mark routes as retryable for those that support idempotent calls (e.g. creating a new file)
- High-level GTable bindings
No significant changes.
- Fix
dx get
untar issue with leading / - Missing
dx-verify-file
andjq
dependencies on Windows
- Support to build of upload agent on RHEL7
- Ability to build and get multi-region apps with custom system requirements
- Environment file so that
source environment
works properly on RHEL7 - Modified
dx-docker
so that--rm
passes through gracefully - Modified
dx-docker
so that theHOME
environment variable defaults to/root
- bug where
dx download
incorrectly interpreted the overwrite option during argument parsing
No significant changes.
- Workflow handler to the Java bindings
- Checksum verification for file downloads in Java
- Bug resulting in transient errors on large downloads
dx-app-wizard
now correctly specifiestimeoutPolicy
dx-docker
now handles default working directory and override properly
- On Mac OS dx-toolkit now supports TLS 1.2 by activating a virtualenv
dx-app-wizard
now defaults to Ubuntu 14.04 as opposed to 12.04- Cosmetic improvements to CLI
describe
andls
subcommands
- Perl and Ruby bindings are no longer supported and associated code has moved to the
dx-toolkit/contrib
directory