materialsproject/MPContribs v3.13.0

on GitHub

Version 3.13.0

Commits

• [c3b2735] client: parallel update_contributions, make_public/private
• [cec535f] testing on dev branch not needed
• [a78498c] Merge pull request #693 from materialsproject/dev
• [373c740] bump kernels and client
• [cb02183] client: add workshop-contribs valid URL
• [d3fa3bb] client: docstring notes
• [50025fb] testing workflow fix
• [1988a00] run test on dev too
• [244baa5] update github actions
• [b06fd97] portal: fix sort request
• [5b355e8] portal: cleaning up, some feature additions
• [6e6ba73] portal: bugfixes for landingpages
• [c2165cc] portal: rm intro dep
• [e68569d] portal: row hover on landingpages
• [ecc2d4b] portal: browse page works well now
• [f4c80ef] api: add endpoint for atlas search on projects
• [0f13d37] portal: more improvements to browse page
• [6d8d413] portal: row hover
• [828db63] portal: much simpler browse page (handsontable)
• [3cd7382] portal: moved browse message to s3 mpcontribs.org
• [e6eae0e] add mpcontribs.org index for s3
• [7bcad1a] portal: start browse revamp with simple table
• [34a6272] portal: remove images
• [a50046d] api: enable filter on attrs for tables
• [203874a] api: define all filters in root document
• [96e5de2] api: get_filter_params in get_specs
• [232015b] api: fix copies for editable installs
• [376096f] update dependencies
• [a45bed2] api: use core FILTERS definition
• [2cbb6ba] api: separate copies for dev subdirs
• [59d9598] client: remove print statement
• [f9c3031] replace _order_by/order with _sort
• [570ed43] client: better regex expansion for param loading
• [33cbfe9] api: support for all operators in swagger specs
• [2229f2a] api: always write swagger specs
• [0154a61] api: consisten filter definitions
• [b78ed04] api: make update stats resilient against OperationFailure
• [c9a6441] api: add stats to project
• [b2a8ab4] api: use dict func to init default
• [b8244a8] api: don't parse quantity if indicated as string in project.columns
• [d679246] client: improve init_columns docstring
• [a154302] default to NWORKERS 2
• [13477db] api: add rq dashboard
• [763451d] add open_catalyst_project NB
• [b205a16] review example notebooks
• [f4db465] bump client, rm implicit deps
• [d69280a] client: use pymongo dep
• [9f7c386] client: bson -> pybson
• [be17028] api: MAX_COLUMNS; protect against inconsistent columns update
• [c745896] bump python image 3.96.3
• [f64a3e6] api: lots of optimizations for speed/efficiency
• [4a3b010] bump client
• [fdc3cd1] client bugfix: make sure cids is list
• [32d7e67] api: use atomic update to save notebook
• [dfd5136] api: revert websocket management
• [60a3d3c] api: restart kernels
• [7a47248] portal: fix code padding
• [78fd975] api: only start dozer for NWORKERS=1
• [d869f09] api: enable dashboard/dozer for prod
• [79bed83] api: add Dozer
• [8f75fa0] nb build: also log error
• [e9e017c] build(deps): bump scipy from 1.7.0 to 1.7.1 in /mpcontribs-portal
• [0d9870d] more dependabot PRs
• [03d8ae4] dependabot PRs
• [4d683cb] api: add dashboard.cfg
• [735878d] api: flask dashboard not connecting in prod
• [44decc2] api: add flask monitoring dashboard
• [bec5fc9] api: only start rq if kernel gateway available
• [d21a14b] add MAX_REQUESTS/JITTER
• [f90af1c] api: try different supervisord.conf dir
• [7d6be7e] api: default job results response for cronjob
• [b11e392] api: dedicated schedulers/queues for each deployment
• [ac0ccff] api: minor logging improvements
• [3ad99c1] api: check number of available kernels
• [44f209d] reserve kernels for each deployment
• [98e8d17] api nb.build: fix client host, close session
• [0c5bea3] bump client
• [6cdbab4] remove supercronic
• [3fced4d] api: use supervisord and flask-rq for NB builds
• [91e2bf1] another citation update
• [4b902e4] update citation file
• [91458f2] add CITATION.cff
• [8174763] raise MAX_BYTES to 1200
• [e08685b] needs_build field
• [f70e50d] api nb.build: reload on demand, fixed timeout
• [f182adc] bump client
• [13d1a4a] enable ml/ls services in docker stack
• [45eec10] rm docker-compose
• [0657fe3] check timestamp on manual build
• [34019db] api: fix gentime check in notebook build
• [d1df686] bump python image 3.96.2
• [aacd74f] kernel-gateway: install ipywidgets
• [512e09d] api: no need to close client in kernel-gateway
• [6d47f1e] dependabot PRs
• [85e115c] nb build force flag
• [ae68b04] client with context
• [372399d] save carrier_transport NB
• [9594439] portal: don't need per_page for get_totals
• [0558baf] api: rebuild NBs by timestamp
• [b559458] api: remove nb pre_delete
• [8b121ec] bump client
• [5ec351d] minor README cleanup
• [7ef748c] client: minor codestyle fix
• [a5e21eb] client: rename per_request param
• [425d4ae] client: no query kwarg necessary
• [0bbdabc] client: use _get_future for deletion
• [d5080db] client: catch closed sessions
• [df34760] client: bugfix _split_query
• [6ce3783] client: cancel requests if not resp.ok; rm while futures
• [aed0a58] client: chunks -> grouper
• [f66bb11] client: use adapater_kwargs for session
• [fc2fd83] client: minor docstring update
• [3e1661f] client: catch/retry rate limited requests
• [c5d0c0f] portal: fix some npm deps
• [04dec57] portal: czmore from npm
• [0940fa2] more dependabot PRs
• [fce9941] portal: noopener noreferrer
• [ab639dd] dependabot PRs
• [4247632] Create codeql-analysis.yml
• [22745ac] client: use assert in test
• [c91bf46] client: use context in tests
• [4d185e5] save carrier_transport notebook
• [a5b13e3] client: codestyle fixes
• [8e9e855] client: return per_page not needed anymore
• [92815b9] client: only retrieve existing contribs if needed
• [79c8a6e] client: _split_query, context manager
• [651a90a] bump client
• [933189a] api: enable and deal with exact operator
• [5b6c4ee] bump client
• [f16c99e] client: save a couple of chars
• [d5c8f8f] client: sets/map format for get_all_ids
• [91f1159] portal: carrier_transport NB update
• [43572f5] portal: carrier_transport NB bugfix
• [6daff4e] portal: save 2dmatpedia NB
• [2e47fde] bump client
• [5543021] client: data_id_field for get_all_ids
• [3fe13de] bump client
• [1811e21] portal: minor detail page css fixes
• [bf0f89b] client: init_columns bug fixes
• [ecc9a78] portal: update transparent_conductors NB
• [dc30863] portal: email on landingpage; cc/subject for mailto
• [45abecb] portal: generate new download version if needed
• [319dcdc] portal: improve external links
• [ca28da3] portal: transparent_conductors NB
• [c31a77c] portal: minor intro text change
• [07bdf18] portal: small notification for empty project on browse
• [c538af3] portal: improve instructions for empty project
• [a638c25] dependabot PRs
• [93d3d01] dependabot PRs
• [a6f9edc] remove code tab, add quick start, use highlight.js
• [9f6afd3] add genesis_efrc_minipipes nb
• [95635b2] portal: warning for data n/a
• [2c3e724] portal: only show download button if data available
• [1ac07db] api: fix bugs innotebook build
• [7458a41] api: projects param and minor fixes for notebook build
• [33edcb6] api: fix approve/deny project
• [ff82dbf] fix URL to code examples
• [a496264] revert kaleido bump
• [5239382] dependabot PRs
• [489361c] bump supercronic
• [b873c79] dependabot supercronic
• [b4fcea0] bump client
• [85e237e] api: improve notebook build
• [1abebd6] client: catch Table display exception
• [d579cb2] remove orca
• [02bd286] bump mpcontribs-client
• [33a4cbb] api: fix notebook builds
• [0bf6397] api: use pid for msgid to avoid duplicate message error
• [76e3616] use kaleido instead of orca
• [eb7199a] pip in-tree-build
• [0d58215] bump python image 3.96.0
• [0db0d8c] client: only forward allowed attrs to Table
• [2b11d88] More dependabot PRs
• [4e850cc] dependabot PRs
• [4f29daf] portal: revert nbconvert; build multiple nbs at once
• [4485278] bump client
• [cfc4263] portal: update notebook
• [8f49cf7] client: bugfix existing dict
• [0b4f450] api: account for custom queryset in project lazyref
• [148f29c] dependabot PRs
• [f56e9bc] client: fix bug with existing in submit_contributions
• [bf5f1c8] client: fix download files count
• [a2004de] client: catch invalid timeout value
• [7976eee] client/portal: support json and csv
• [92eeaac] api: json/csv for all components
• [1b588cb] dependabot PRs
• [e8f412a] portal: downloads on browse page
• [9ab89f3] portal: table download buttons
• [3318b21] portal: final downloads testing
• [50c3e01] yay downloads
• [5d586a0] api: change contributions limits
• [72ceb48] client: cumulative timeout for download
• [42b7dc6] client: _get_per_page_default_max
• [d6b279a] dependabot PRs
• [e0cb98d] client: also remove ratelimit from setup.py
• [7a50780] client: minor flake fixes
• [1e59abe] client: timeout, _run_futures hook
• [329e2f6] client: get_session()
• [23cc9f0] client: remove ratelimit
• [8bd0280] api: only calc total_data_pages if total_data_rows set
• [e5a069c] portal: some landingpage cleanup
• [16a4957] dependabot PRs
• [890f8cc] portal: make sure landing page title fits
• [0b38c57] portal: keep project in download query
• [e36084b] portal: multiline browse page; add download buttons
• [adf08f8] api: account for custom queryset manager in bulma_* fields
• [d4c25d2] client: add bson dep to setup.py
• [3c2eb49] portal: add project download button
• [31bda69] portal: minor fix in cards nb
• [c64ac4e] portal: _zip_download
• [32e864f] MORE_PIP_FLAGS
• [c0048dd] portal: finally a download_project view
• [c30d30c] client: also check host on client re-init
• [736559c] client: add content-type to tests
• [028fbd9] client: fix tests
• [8faf5ac] api: paginate projects
• [b3b22ad] client: test and improve download_contributions()
• [4b249a7] dependabot PRs
• [3c9125a] client: parallel download requests
• [b5d896c] more dependabot PRs
• [b9b3761] dependabot PRs
• [69b333b] client: remove max_workers kwarg
• [5a56331] api/client: better per_page handling
• [c7ebfee] client: overhaul for download_contributions()
• [276bdc1] portal: update download_contribution
• [4ca743e] bump mpcontribs-client
• [ff14edc] portal: fix nb related resource
• [3a59909] client: include kwarg to control components download
• [35c59af] client: download_contribution()
• [fde937d] enable downloading components
• [556b95b] bump apispec and tqdm
• [2f28c73] bump boto3
• [0f747f3] dependabot PRs
• [65cbd88] add cards notebook
• [2d53bed] api: queryset_manager for only fields; notebook Ref
• [8eee5c1] api: fix flask-mongorest branch
• [ac72b70] bump client
• [7ff0369] client: flake8 bugfix
• [a750011] client: validate payload, update_contributions(), publish()
• [5c04b40] bump python image 3.95.1
• [dc2b64c] last dependabot PRs for today
• [098e392] more dependabot PRs
• [27cfd31] dependabot PRs
• [5da9a89] client: use get_model for field definitions
• [34f6e9b] client: docstrings and dir for autocomplete
• [3548033] bump client
• [a26108f] client: fix flake8 error
• [3dcb83a] client: Attachment.from_data()
• [6ef5a86] portal: component modals
• [670b42b] bump client
• [f8c4e8d] client: use tqdm.auto import
• [4ad0705] client: check ipython in component display
• [cf7418f] portal: adjust to new client
• [6d1ac44] bump client
• [d9d6d7c] client: minor docstring additions
• [b3bc3b5] client: uniform component functions
• [2943441] client: Structure -> PmgStructure
• [34c2312] portal: only link ObjectIds in id field
• [593b13b] portal: minor landing page layout fixes
• [1fb1041] bump python image 3.95.0
• [f653150] dependabot PRs
• [2727a09] moar dependabot PRs
• [bdf0b89] dependabot PRs
• [d0f0919] client: README fix
• [c561c93] bump client
• [0d918f9] notebook updates
• [bf0fc0d] client: propagate table attrs
• [1e1e725] client: inf_as_na; pd.to_numeric, fillna empty strings
• [221ca7e] api: fix format_cell for empty strings, use nominal_value
• [d39c090] api: catch nan's in tables
• [ff9f1e3] client README typo fix
• [d26be9d] bump client
• [bf3a64c] client: bravado fork in README
• [328f575] update lightsources get_started NB
• [b7a1b3b] api: new client display, add attachments
• [758254d] adjust notebooks to client display
• [ed7f2e4] bump client
• [0c9a957] client: display/info for components
• [b82ad55] client: initial_total not needed
• [380c9da] fix component duplicate checks and referencing
• [f3d0975] api: attachment contents must be str
• [5281ccb] client: bugfix to keep duplicates for submission
• [bf58b37] client: bugfix id2project for updates
• [ad6b42e] api: null=True for all component updates
• [b52ae48] client: use last_modified to calc updated total
• [221c9e0] api: move last_modified to pre save
• [7a08a0a] bump python image 3.94.2
• [90e697d] api: use Before/After op for last_modified
• [bf356b6] api/client: update contribution components
• [5c298e5] boto3 bump
• [a3dcd03] dependabot PRs
• [524996d] bump client
• [7ba5d88] client: fail safes for init_columns; allow reordering
• [8c12581] api: include field in unit warning
• [1cda80e] bump python image 3.94.1
• [cb6b316] dependabot PRs
• [d0ffe56] bump client
• [d727a6f] client: include some sanity checks for init_columns
• [44b650f] api: set sensible bulk_update_limit for contributions
• [e45239f] bump client
• [4f21b8f] bump orca
• [8ad55b2] api: fix notebook builds
• [3c9e60c] client.init_columns: add dimensionless quantity example
• [81fa8f5] bump client
• [50f031f] fix code style errors
• [45c0ff0] client: higher limit for error msg cutoff
• [e1e0cf8] api: add attachment name to S3 metadata
• [c18ccea] api: only retrieve S3 attachments when needed
• [94bb8d4] api: marshmallow-mongoengine 0.30.2
• [a398950] client: better print errors
• [5e402ad] bump python image
• [0c1e65e] build(deps): bump jupyter-client in /mpcontribs-portal
• [0fbb83b] dependabot PRs
• [1bb99b2] api: use API_CNAME for attachment keys in S3
• [07ee45a] portal: show errors in overview table
• [ab130a0] client: better docstrings/messages; multiple projects in submit_contributions; unflatten data
• [f8d8488] client: Client/init_columns docstrings
• [5ce1556] client: clean up order in init_columns
• [94c0928] portal: raw/without_components downloads
• [5c34625] build(deps): bump django from 3.1.7 to 3.1.8 in /mpcontribs-portal
• [0c389d1] bump python image
• [1159b57] client: bump bravado commit
• [ea5a252] dependabot PRs
• [b592a8b] client: fix code style errors
• [31399b6] portal: add attachments to search
• [70abf0a] portal: implement attachments
• [a5ab539] client: get_attachment convenience function
• [83f9ac9] api: validate base64 encoding for attachment content
• [6de74a2] api: avoid getting attachment from S3 unless content requested
• [158b1dc] api: supported file types for attachments
• [f46a5b8] client: add support for attachments
• [aaa7982] api: implement attachments
• [2b43a87] client: add localhost.*.materialsproject.org as valid urls
• [bbb8458] bump python image
• [209e867] bump client
• [67bb9a6] dependabot PRs
• [2cf3ee2] bump client
• [44a3398] client: fix allowed ports
• [e2fec46] portal: fix login href
• [d8f3513] pymatgen bump
• [1288bc5] dependabot PRs
• [a8e582a] bump client
• [72726a5] client: minor README formatting
• [38c03ef] client: another shot at getting test working
• [e12587f] client: fix env export in windows
• [5b3e16b] client: SSL_CERT_FILE is passed on automatically
• [cabbb74] client: try export SSL_CERT_FILE explicitly for windows
• [1c28995] client: allow externals for ubuntu/windows testing
• [4b05785] client: add troubleshoot section to README
• [d1edfa5] client: set SSL_CERT_FILE for tests
• [8c0d91b] client: bump twisted and bravado
• [c3de277] client: update tests
• [3fc860b] client: check valid URLs
• [a82bbae] dependabot PRs
• [c902624] bump client
• [01c16d0] dependabot PRs
• [111a264] remove pymatgen root-level imports
• [f7cb1fd] dependabot PRs
• [5ed71b2] devops:python-3.92.0
• [003781a] build(deps): bump boto3 from 1.17.12 to 1.17.13 in /mpcontribs-api
• [7eccfe6] dependabot PRs
• [6862b75] perovskites_diffusion notebook
• [b6d9a05] bioi_defects notebook
• [2898d08] bump client
• [1acadf4] client: fix protocol criterium
• [1ae00e3] portal: only dropdown at navbar-end
• [ac5a46f] portal: include profile info (auto-redirect in grant
• [9276144] portal: add intro text to browse page
• [9ca4e5d] work -> code; apply -> contribute
• [c033efb] portal: hyperlink login in alert message
• [9c0bc2a] docker docs to devops
• [cc45e54] redirect root to browse
• [b445a67] docs.mpcontribs.org
• [59df520] api: strip whitespace in groups
• [5e8931e] api: fixed has_read_permissions
• [2c3686c] dependabot PRs
• [cad8534] api: progress on fixing read access
• [46ae58d] portal: catch not found exceptions
• [4122599] oauth -> profile
• [4bebe8a] bump client
• [4811d6f] client: ensure only single colon in username
• [d2fcc88] api: register ProviderEmailField, add Validator
• [37219de] api: include kernels in healthcheck only for prod
• [aa06f64] portal: don't use look-aheads
• [69d1def] api health: include app.kernels check
• [9e79384] portal: switch to sass
• [70eec96] portal: trying to fix download notification
• [3460aa4] portal: switch to yarn for node packages
• [fea3834] dependabot PRs
• [616c104] portal: done with anonymous responses
• [b32f988] portal: anonymous download response
• [b889c7b] bump pymatgen in /mpcontribs-sidecars/kernel_gateway
• [87107f8] bump client
• [adb0378] portal: working on anonymous responses
• [39cca14] client: use colon to decide on protocol
• [7bb1bdf] api/portal: allow access to public projects for anonymous
• [55f79e8] dependabot PRs
• [740794c] api: catch empty strings in groups
• [c505831] bump client
• [c43cffd] api: ProviderEmailField for project owner
• [4f17080] client: decide protocol by localhost in host
• [397dfc0] portal: add explicit redirects for old project names
• [6ebad2b] portal: Login/Profile button
• [9895256] rm console log and profile info
• [b3a3fdf] portal: contribs-web allowed host and referrer policy
• [441ac12] portal: OAUTH_URL; minor header_footer stuff
• [50116bd] portal: upgrade to webpack5 and latest dependencies
• [9ff5975] client: fix email/username validation
• [8130433] api: fix SNS client endpoint/email
• [6cc5842] api: remove login route
• [b06505d] make better decisions based on CNAME
• [e13d20d] bump devops/python
• [dfc3045] dependabot PRs
• [a62e3a9] portal: mjs bugfix, few version bumps
• [97baf43] move prep.sh out of the way
• [520db9b] bump client
• [f84ef6a] client.reqs: pin commits, add twisted
• [9ee0c41] client: flake fix, remove py36
• [a83aca9] client: tox add py36
• [b3e6090] client: add live client test
• [e2f2da2] client: include macos/windows in tests
• [3ed2207] client: use bravado fork with threading.TIMEOUT_MAX
• [e721ad5] bump client
• [c63854b] dependabot PRs
• [4168e55] bump client
• [5ca868b] portal: screening_inorganic_pv NB ok
• [9280311] client: get table by tid or md5
• [57c0c4e] dependabot: only run on mpcontribs-client path
• [0f4783d] bump client
• [ea07c70] client: retry flag, submit docstring
• [9ae6a16] portal: target blank for login
• [548d8a1] update screening_inorganic_pv notebook
• [c5bf699] portal: copy from python3.9
• [e8e699e] remove api key clipboard button
• [3f34472] api: bugfix schema2jsonschema
• [165a21f] dependabot PRs
• [211d30a] deployments: fix api host
• [96d47b9] api: bump reqs, rm npm, py39
• [7a6cbde] api dockerignore
• [e39995c] gh action: fetch-depth to retrieve all tags
• [f806ec3] gh action: build package in publish job
• [8c7a4b6] gh action: separate publish job
• [7481fda] gh action: test multiple python versions
• [8ccaf22] kernel-gateway py39
• [3b6077c] bump mpcontribs-client
• [b139320] compose: moving to devops repo
• [28f826e] portal: add screening_inorganic_pv notebook
• [6a25615] save TODOs
• [31457ad] bump orca
• [643b36a] docs: add link to workshop lesson
• [b73145d] api: use flasgger repo
• [b54f022] tox: add py39
• [695841a] devops/python 3.90.10
• [5dc99b2] bump client
• [f81cb09] more dependabot PRs
• [3ca6034] dependabot PRs
• [944bb52] bump client
• [3b030d9] dependabot PRs
• [2a2c2cc] remove logout button
• [4da9e3b] portal: update login/profile link; add groups and logout
• [2150828] bump client
• [5a03968] mpcontribs.org -> contribs.materialsproject.org
• [5afe58c] portal: oauth login and profile
• [cc392a7] also user X-Consumer-Groups
• [383e793] build(deps): bump boto3 from 1.16.35 to 1.16.36 in /mpcontribs-api
• [f95cef3] dependabot PRs
• [1dbcd20] adjust headers for kong-proxy-oauth
• [6ad948b] bump client
• [f447416] more dependabot PRs
• [f73a5e1] dependabot PRs
• [58d5535] api nb.build: estimated_doc_count; unset missing NBs
• [78f7cca] bump client
• [17892d3] dependabot PRs
• [64a4fb3] portal: can't comment things out in JSON
• [fdd04aa] build(deps): bump boto3 from 1.16.23 to 1.16.24 in /mpcontribs-api
• [0923ea7] dependabot PRs
• [aaf6118] portal: mathjs not needed rn
• [c2b42ad] bump client
• [b75fa3a] client: allow empty string as unit for dimensionless
• [d5f8966] bump client
• [000d75a] client: allow name to be set for structures
• [551a345] build(deps): bump boto3 from 1.16.13 to 1.16.16 in /mpcontribs-api
• [d1c8bec] client: don't resubmit if unique_identifiers=False
• [bc5a08e] dependabot PRs
• [b66072c] api: allow to be used w/o SNS and Kernel Gateway
• [b7314b3] dependabot PRs
• [487d8cd] cloudformation moved to devops
• [05f0129] cfn: kong session secret
• [e32b544] portal: save 2dmatpedia NB
• [8f2a0e0] bump client
• [59abc01] client: only use index for component name if necessary
• [327caf7] api: fix notebook deletion for lazy reference
• [a88b76d] portal: note on spam folder during apply
• [c63c53b] portal: revert to node 14; sort package.json
• [96fbb77] dependabot PRs
• [dbe9c39] cfn: adjust NUM_WORKERS for MP
• [d364b26] portal-ls: update get_started notebook
• [7c50572] bump client
• [427012d] client.get_contribution: don't return notebook field
• [bdf50f5] api: only check dangling NBs if necessary