diff options
Diffstat (limited to 'issues')
30 files changed, 201 insertions, 23 deletions
diff --git a/issues/binderlite/add-configuration-to-set-server-name.gmi b/issues/binderlite/add-configuration-to-set-server-name.gmi index d54997c..4181f17 100644 --- a/issues/binderlite/add-configuration-to-set-server-name.gmi +++ b/issues/binderlite/add-configuration-to-set-server-name.gmi @@ -1,8 +1,14 @@ # Add configuration to set server name +## Tags + * assigned: jgart +* type: feature-request +* status: unclear +* priority: high +* keywords: binderlite, notebooks, configuration -* feature +## Description Let's use environment variables as configuration diff --git a/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi b/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi index 035fb76..4640c1c 100644 --- a/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi +++ b/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi @@ -1,6 +1,13 @@ -* bug +# Add Regular Expression to Prevent Invalid Input +## Tags +* type: bug * assigned: jgart +* status: unclear +* keywords: binderlite, notebooks +* priority: high + +## Description Add regex to the html form to prevent the user from submitting an invalid git repo url or other string. diff --git a/issues/binderlite/ansi2html_terminal_user_feedback.gmi b/issues/binderlite/ansi2html_terminal_user_feedback.gmi index 969448a..c0cba55 100644 --- a/issues/binderlite/ansi2html_terminal_user_feedback.gmi +++ b/issues/binderlite/ansi2html_terminal_user_feedback.gmi @@ -1,8 +1,12 @@ # ansi2html terminal user feedback -* ongoing -* feature-request +* status: ongoing, in progress +* type: feature-request * assigned: jgart +* priority: medium +* keywords: binderlite, notebooks, ansi2html + +## Description https://builds.sr.ht/~sircmpwn/job/610711 diff --git a/issues/binderlite/finds-unknown-package-in-manifest.gmi b/issues/binderlite/finds-unknown-package-in-manifest.gmi index 1bcba39..cf1d25b 100644 --- a/issues/binderlite/finds-unknown-package-in-manifest.gmi +++ b/issues/binderlite/finds-unknown-package-in-manifest.gmi @@ -30,4 +30,10 @@ Or, should channels be managed by the sysadmin only for security reasons? It's probably a security risk since a guix channel can pull in arbitrary packaged code that might not be audited or fully trusted. -* bug +## Tags + +* type: bug +* assigned: jgart +* status: unclear +* keywords: binderlite, notebooks +* priority: high diff --git a/issues/binderlite/integrate-styling-with-gn2.gmi b/issues/binderlite/integrate-styling-with-gn2.gmi index dc158fa..e2d5843 100644 --- a/issues/binderlite/integrate-styling-with-gn2.gmi +++ b/issues/binderlite/integrate-styling-with-gn2.gmi @@ -1,7 +1,12 @@ # Integrate styling of app with GN2 -* ongoing +* status: ongoing, in progress * assigned: jgart +* type: bug +* priority: medium +* keywords: binderlite, notebooks, styling, UI + +## Description Currently using antiweb for styling with modifications. diff --git a/issues/binderlite/kernel-dying.gmi b/issues/binderlite/kernel-dying.gmi index 07017f2..25008de 100644 --- a/issues/binderlite/kernel-dying.gmi +++ b/issues/binderlite/kernel-dying.gmi @@ -1,5 +1,15 @@ # R Kernel Dying +## Tags + +* assigned: jgart +* type: bug +* priority: high +* status: unclear +* keywords: R + +## Core Dump + ``` [I 08:45:24.502 NotebookApp] Writing notebook-signing key to /home/jgart/.local/share/jupyter/notebook_secret [W 08:45:24.515 NotebookApp] Notebook 2020-05-08/solberg-rat-analysis.ipynb is not trusted diff --git a/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi index 49f5d3f..b734f5c 100644 --- a/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi +++ b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi @@ -1,7 +1,13 @@ # Return canned text if notebook description returns none -* bug? +## Tags +* type: bug * assigned: jgart +* priority: high +* status: in progress +* keywords: binderlite, notebooks + +## Description Notebooks that do not have a description will use python's `None` value as the project's description. @@ -23,3 +29,7 @@ if notebook.description == None: ``` WDYT? + +### 2022-03-16 fredm + +I like the first one better diff --git a/issues/binderlite/use-root-file.gmi b/issues/binderlite/use-root-file.gmi index 21a7ac5..aa2978c 100644 --- a/issues/binderlite/use-root-file.gmi +++ b/issues/binderlite/use-root-file.gmi @@ -1,4 +1,18 @@ - # guix shell --root +# Guix: Using guix shell with root file + +## Tags + +* assigned: jgart +* type: unclear +* status: unclear +* priority: low +* keywords: guix, guix shell, root file + +## Description + +``` +guix shell --root +``` Let's benchmark and test these options to see if it helps the speed/times with building a new container. diff --git a/issues/deploy.gmi b/issues/deploy.gmi index 94d73ec..35e707c 100644 --- a/issues/deploy.gmi +++ b/issues/deploy.gmi @@ -13,7 +13,11 @@ settings; and removing this would make gn2 as is disfunctional. # Tags -* assigned: bonfacem +* assigned: bonfacem, fredm +* type: bug +* priority: medium +* status: in progress +* keywords: GN2, configuration, deploy # Notes diff --git a/issues/gemma/HS-Rat-crashes-gemma.gmi b/issues/gemma/HS-Rat-crashes-gemma.gmi index 5d0171a..316e1a3 100644 --- a/issues/gemma/HS-Rat-crashes-gemma.gmi +++ b/issues/gemma/HS-Rat-crashes-gemma.gmi @@ -7,6 +7,10 @@ Running GEMMA on the NSNIH dataset in Genenetwork sends the server in a tail spi ## Tags * assigned: pjotrp, zachs +* status: unclear +* type: bug +* priority: high +* keywords: gemma, crash ## Tasks diff --git a/issues/gemma/databases-getting-out-of-wack.gmi b/issues/gemma/databases-getting-out-of-wack.gmi index 5e4fc1c..a102846 100644 --- a/issues/gemma/databases-getting-out-of-wack.gmi +++ b/issues/gemma/databases-getting-out-of-wack.gmi @@ -1,10 +1,14 @@ # Databases Getting Out of Wack -## Let's use Gemma instead of Reaper +## Tags * assigned: Bonface, Zach, jgart * priority: high -* bug +* type: bug +* status: unclear +* keywords: database, gemma, reaper + +## Let's use Gemma instead of Reaper Zachary: > If we're using GEMMA, we'll need to recalculate all other trait Max LRS scores using diff --git a/issues/genenetwork/api-docs.gmi b/issues/genenetwork/api-docs.gmi index 8805cc4..e9fbc92 100644 --- a/issues/genenetwork/api-docs.gmi +++ b/issues/genenetwork/api-docs.gmi @@ -6,4 +6,5 @@ Here's a simple way that SourceHut documents their API endpoints with markdown. ## Tags -* docs +* type: documentation +* keywords: GN3 diff --git a/issues/genenetwork/environment.gmi b/issues/genenetwork/environment.gmi index 00105be..e66550f 100644 --- a/issues/genenetwork/environment.gmi +++ b/issues/genenetwork/environment.gmi @@ -9,3 +9,7 @@ It somehow got reverted and is out of date. Please see if we can get a list agai ## Tags * assigned: bonfacem +* type: bug +* status: unclear +* priority: medium +* keywords: guix, packages, environments diff --git a/issues/genenetwork/genewiki.gmi b/issues/genenetwork/genewiki.gmi index e7096dc..e0a0a00 100644 --- a/issues/genenetwork/genewiki.gmi +++ b/issues/genenetwork/genewiki.gmi @@ -19,6 +19,9 @@ with an edit button, similar to ## Tags * assigned: pjotrp, zsloan -* enhancement +* type: enhancement +* priority: medium +* status: unclear +* keywords: GN1, documentation ## Tasks diff --git a/issues/genenetwork/global-search.gmi b/issues/genenetwork/global-search.gmi index 01d9c0f..a39da80 100644 --- a/issues/genenetwork/global-search.gmi +++ b/issues/genenetwork/global-search.gmi @@ -5,6 +5,10 @@ Global search is the top bar of GN2 ## Tags * assigned: pjotrp, zsloan +* status: unclear +* priority: critical +* type: bug +* keywords: global search, BRCA2 ## Tasks diff --git a/issues/genenetwork/http-https.gmi b/issues/genenetwork/http-https.gmi index 80306bf..9777185 100644 --- a/issues/genenetwork/http-https.gmi +++ b/issues/genenetwork/http-https.gmi @@ -12,4 +12,10 @@ if ($scheme = http) { } ``` +## Tags + * assigned: pjotr, arthur, jgart +* type: bug +* priority: medium +* status: unclear +* keywords: GN2, http, https diff --git a/issues/genenetwork/proxy-hard-coded.gmi b/issues/genenetwork/proxy-hard-coded.gmi index ab4c974..f9a7b18 100644 --- a/issues/genenetwork/proxy-hard-coded.gmi +++ b/issues/genenetwork/proxy-hard-coded.gmi @@ -25,3 +25,7 @@ wqflask/utility/authentication_tools.py # Tags * assigned: bonfacem, pjotrp, zachs +* type: bug +* priority: medium +* status: unclear +* keywords: proxy, configuration, settings diff --git a/issues/genenetwork/remove-elasticsearch.gmi b/issues/genenetwork/remove-elasticsearch.gmi index c484ca1..461423f 100644 --- a/issues/genenetwork/remove-elasticsearch.gmi +++ b/issues/genenetwork/remove-elasticsearch.gmi @@ -2,6 +2,14 @@ We are no longer using that database +Seems related to + +=> ../issues/remove-elastic-search.gmi + ## Tags * assigned: bonfacem +* type: enhancement +* priority: low +* status: unclear +* keywords: elasticsearch, purge diff --git a/issues/genenetwork1/gn1-symbols.gmi b/issues/genenetwork1/gn1-symbols.gmi index ac4cf71..1bc3606 100644 --- a/issues/genenetwork1/gn1-symbols.gmi +++ b/issues/genenetwork1/gn1-symbols.gmi @@ -3,6 +3,10 @@ # Tags * assigned: pjotrp, arthurc +* type: bug +* priority: medium +* status: unclear +* keywords: GN1, symbols # Tasks diff --git a/issues/gn3-technical-debt.gmi b/issues/gn3-technical-debt.gmi index 189b756..a31012f 100644 --- a/issues/gn3-technical-debt.gmi +++ b/issues/gn3-technical-debt.gmi @@ -1,6 +1,12 @@ +# GN3: Technical Debt + ## Tags * assigned: bonfacem +* priority: medium +* status: in progress +* type: enhancement +* keywords: GN3 ### Introduction diff --git a/issues/gnbug/add-convenience-templates.gmi b/issues/gnbug/add-convenience-templates.gmi index 41eb975..29f266a 100644 --- a/issues/gnbug/add-convenience-templates.gmi +++ b/issues/gnbug/add-convenience-templates.gmi @@ -1,6 +1,14 @@ -# Add convenienve templates +# Add convenience templates -* feature-request +## Tags + +* assigned: jgart +* type: feature-request +* priority: low +* status: in progress, discussion, stalled +* keywords: tissue, gnbug + +## Description WDYT of adding a subcommand called `report` to generate a template for a bug report? diff --git a/issues/gnbug/hide-stale-issues.gmi b/issues/gnbug/hide-stale-issues.gmi index b07fc5d..3184fdc 100644 --- a/issues/gnbug/hide-stale-issues.gmi +++ b/issues/gnbug/hide-stale-issues.gmi @@ -2,4 +2,10 @@ Our list of issues are growing by the day. And, for some reason, we are not eager to close many of them. :-P This makes the command-line output long. Maybe, hide stale issues by default, and show them only if some --all flag is passed. Stale issues are tentatively defined as those issues that have been inactive for more than 6 months. +## Tags + * assigned: bonfacem, aruni +* type: enhancement, feature-request +* status: unclear +* priority: low +* keywords: tissue, gnbug diff --git a/issues/gnbug/recent-first-sort.gmi b/issues/gnbug/recent-first-sort.gmi index 229554a..983b224 100644 --- a/issues/gnbug/recent-first-sort.gmi +++ b/issues/gnbug/recent-first-sort.gmi @@ -2,7 +2,13 @@ Add a command-line option --sort=(newest-first|oldest-first) to gnbug that determines the order the issues are listed. oldest-first is useful for command-line usage where you don't want to scroll up to see the most recent issue. newest-first is useful when generating gemtext/web pages where you don't want to scroll down to see the most recent issue. +## Tags + * assigned: bonfacem +* type: enhancement, feature-request +* priority: medium +* status: stalled +* keywords: tissue, gnbug # INFO diff --git a/issues/per-service-profile-for-shepherd-services.gmi b/issues/per-service-profile-for-shepherd-services.gmi index b22448b..654a723 100644 --- a/issues/per-service-profile-for-shepherd-services.gmi +++ b/issues/per-service-profile-for-shepherd-services.gmi @@ -31,3 +31,11 @@ Currently there are a bunch of shepherd services (on Penguin2, as user shepherd) * power * rn6app * singlecell + +## Tags + +* assigned: efraim +* type: bug +* status: unclear +* priority: high +* keywords: shepherd, system administration diff --git a/issues/quality-control/enumerate-all-qc-checks.gmi b/issues/quality-control/enumerate-all-qc-checks.gmi index 2f72f24..90addc5 100644 --- a/issues/quality-control/enumerate-all-qc-checks.gmi +++ b/issues/quality-control/enumerate-all-qc-checks.gmi @@ -1,7 +1,12 @@ +ume # Enumerating all QC checks We need to enumerate all QC checks and platforms that we want to test against. -* assigned: jgart, arthur +## Tags -* in progress +* assigned: jgart, arthur +* status: in progress +* type: feature-request +* priority: high +* keywords: quality control diff --git a/issues/redis-data.gmi b/issues/redis-data.gmi index 2246c96..995ef1e 100644 --- a/issues/redis-data.gmi +++ b/issues/redis-data.gmi @@ -3,4 +3,12 @@ ATM how we store data in redis is undocumented. Without this, it's hard for contributors to work out how to modify some things. For example, PJ would want to add himself to the editors group. Doing -this was non-trivial for him.
\ No newline at end of file +this was non-trivial for him. + +## Tags + +* type: bug +* priority: high +* assigned: bonfacem +* status: unclear +* keywords: documentation, data, redis diff --git a/issues/remove-elastic-search.gmi b/issues/remove-elastic-search.gmi index af475d6..49b2385 100644 --- a/issues/remove-elastic-search.gmi +++ b/issues/remove-elastic-search.gmi @@ -7,9 +7,15 @@ in gn2. ## Tasks * assigned: bonfacekilz -* keywords: chore, done +* keywords: chore, elasticsearch +* status: done, completed, closed +* type: bug ## Notes While at it, "@depracated" was removed since it added extra noise to -the logs.
\ No newline at end of file +the logs. + +Seems related to + +=> genenetwork/remove-elasticsearch.gmi diff --git a/issues/resurrect-mechanical-rob.gmi b/issues/resurrect-mechanical-rob.gmi index 7b12f0d..bea2a78 100644 --- a/issues/resurrect-mechanical-rob.gmi +++ b/issues/resurrect-mechanical-rob.gmi @@ -2,4 +2,10 @@ We need to run Mechanical Rob tests as part of our continuous integration tests. Mechanical Rob has not been run in a while, and I'm not sure the Mechanical Rob code in the genenetwork2 repository is complete. Get it running again and document the process. +## Tags + * assigned: bonfacem, aruni +* keywords: testing, CI, CD, mechanical rob +* status: in progress +* type: enhancement +* priority: medium diff --git a/issues/slow-correlations.gmi b/issues/slow-correlations.gmi index 955800c..9f4c8c8 100644 --- a/issues/slow-correlations.gmi +++ b/issues/slow-correlations.gmi @@ -2,10 +2,15 @@ Correlations for huge data set(like the exo dataset) is very slow; and the UI crashes. -## Tasks +## Tags +* type: bug +* priority: critical * assigned: bonfacekilz, alex -* keywords: critical bug, in progress +* keywords: correlations, ui, crash +* status: in progress + +## Tasks * [ ] Caching slow queries * [ ] Server side pagination @@ -104,4 +109,4 @@ time to compute. According to Rob, GN1 does not rely on a cache. Instead it is computing from a materialized view of the database that is -intentionally designed for a fast web service.
\ No newline at end of file +intentionally designed for a fast web service. diff --git a/issues/zero-repr-in-data-upload.gmi b/issues/zero-repr-in-data-upload.gmi index b283add..f8143e8 100644 --- a/issues/zero-repr-in-data-upload.gmi +++ b/issues/zero-repr-in-data-upload.gmi @@ -1,6 +1,12 @@ +# Data Uploads: Zero Representation + ## Tags * assigned: bonfacem +* type: bug +* priority: high +* status: in progress +* keywords: data uploads ### Introduction |