Ecosyste.ms: Issues

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GitHub / kalekundert/stepwise issues and pull requests

#73 - Add "output suffix" option to `sw go`

Issue - State: closed - Opened by kalekundert about 2 years ago

#72 - Add commands to skip previous steps

Issue - State: closed - Opened by kalekundert about 2 years ago

#71 - Represent protocol steps as a task graph

Issue - State: open - Opened by kalekundert over 2 years ago - 4 comments

#70 - Give protocols a "warnings" section

Issue - State: open - Opened by kalekundert over 2 years ago - 1 comment

#68 - Allow non-linear master mix setups

Issue - State: closed - Opened by kalekundert over 2 years ago

#67 - Option to group reagent in master mixes

Issue - State: open - Opened by kalekundert over 2 years ago - 1 comment

#65 - Share column widths between reaction tables in `Reactions`

Issue - State: open - Opened by kalekundert over 2 years ago - 1 comment

#64 - Option to calculate master mix stock concentrations

Issue - State: closed - Opened by kalekundert over 2 years ago

#63 - Add a wellmap plugin

Issue - State: open - Opened by kalekundert over 2 years ago

#62 - Teach `Reactions` about replicates

Issue - State: closed - Opened by kalekundert over 2 years ago

#61 - Allow reactions to set multiple scales

Issue - State: closed - Opened by kalekundert over 2 years ago

#60 - Refactor `Reaction`

Issue - State: closed - Opened by kalekundert over 2 years ago - 1 comment

#59 - Allow multi-step master mixes

Issue - State: closed - Opened by kalekundert over 2 years ago - 1 comment

#58 - Refactor the internal protocol representation

Issue - State: open - Opened by kalekundert over 2 years ago

#57 - Allow reactions to mix units

Issue - State: open - Opened by kalekundert over 2 years ago

#56 - Merge identical footnotes

Issue - State: closed - Opened by kalekundert over 3 years ago - 1 comment

#55 - Changing a reagent key should not affect ordering

Issue - State: closed - Opened by kalekundert over 3 years ago

#54 - Make it possible to convert between reagents and solvents

Issue - State: closed - Opened by kalekundert over 3 years ago - 1 comment

#53 - Fix coveralls

Issue - State: open - Opened by kalekundert over 3 years ago

#52 - Allow protocols to output directly to stdout

Issue - State: open - Opened by kalekundert over 3 years ago - 1 comment

#51 - Match partial preset names

Issue - State: open - Opened by kalekundert over 3 years ago

#49 - Parse config schema from usage text

Issue - State: open - Opened by kalekundert over 3 years ago - 1 comment

#48 - Allow a preset to inherit from a preset with the same name

Issue - State: closed - Opened by kalekundert over 3 years ago

#47 - Better error message for non-existent preset names

Issue - State: open - Opened by kalekundert over 3 years ago

#46 - Add a `definition_list` formatting object

Issue - State: closed - Opened by kalekundert over 3 years ago - 3 comments

#45 - Standardized way of specifying reagents

Issue - State: open - Opened by kalekundert over 3 years ago

#44 - Allow numbers and spaces in units

Issue - State: open - Opened by kalekundert almost 4 years ago - 1 comment

#43 - `sw step`: Add syntax for specifying subsubsteps

Issue - State: closed - Opened by kalekundert almost 4 years ago

#42 - Add a `reaction` command

Issue - State: closed - Opened by kalekundert almost 4 years ago

#41 - Can't use `sw note` after protocol that uses `Step` objects.

Issue - State: closed - Opened by kalekundert almost 4 years ago

#40 - Print usage text (i.e. --help) to stderr

Issue - State: closed - Opened by kalekundert almost 4 years ago

#39 - Don't check footnotes until protocol is printed?

Issue - State: open - Opened by kalekundert almost 4 years ago - 2 comments

#38 - Don't count indentical protocols as duplicates

Issue - State: open - Opened by kalekundert about 4 years ago

#37 - Allow adding objects with a 'protocol' attribute to protocols.

Issue - State: closed - Opened by kalekundert about 4 years ago - 1 comment

#36 - Accept "Conc" column in MasterMix.from_text()

Issue - State: closed - Opened by kalekundert about 4 years ago

#35 - More sophisticated formatting objects

Issue - State: closed - Opened by kalekundert about 4 years ago - 4 comments

#34 - Rename Protocol.show() to Protocol.format()

Issue - State: closed - Opened by kalekundert about 4 years ago

#33 - Easy way to produce pickles from python protocols

Issue - State: closed - Opened by kalekundert about 4 years ago

#31 - Make `stash pop` hide rather than delete

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#30 - Add `stepwise stash replace <id>` command.

Issue - State: closed - Opened by kalekundert over 4 years ago - 3 comments

#29 - Add "Dependencies" column to `stash`

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#28 - Automatically wrap long lines in reaction tables.

Issue - State: closed - Opened by kalekundert over 4 years ago - 4 comments

#27 - Add `note` command to add footnotes via CLI

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#26 - Allow reactions specified by text to not have a solvent.

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#25 - Simplify the arguments to load()

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#24 - Merge identical footnotes.

Issue - State: closed - Opened by kalekundert over 4 years ago

#23 - Allow plugins to make use of the config file.

Issue - State: closed - Opened by kalekundert over 4 years ago

#22 - Escape newlines in command header

Issue - State: closed - Opened by kalekundert over 4 years ago

#21 - Think about renaming `split`

Issue - State: closed - Opened by kalekundert over 4 years ago

#20 - Make it possible to set the date

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#19 - Cache information in pickles to speed up pipelines.

Issue - State: closed - Opened by kalekundert over 4 years ago

#18 - Truncate long commands when printing

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#17 - Support nested stepwise commands

Issue - State: closed - Opened by kalekundert over 4 years ago - 1 comment

#16 - `cd` command

Issue - State: closed - Opened by kalekundert almost 5 years ago - 1 comment

#15 - Make "error parsing stdin" smarter.

Issue - State: closed - Opened by kalekundert almost 5 years ago

#14 - Issue a warning if a protocol is empty.

Issue - State: closed - Opened by kalekundert almost 5 years ago

#13 - Give reagents separate "names" and "keys"

Issue - State: closed - Opened by kalekundert almost 5 years ago

#12 - Specify subdirectories in protocol slugs

Issue - State: closed - Opened by kalekundert almost 5 years ago - 2 comments

#11 - Use JSON to communincate through pipes.

Issue - State: closed - Opened by kalekundert almost 5 years ago

#10 - Provide way to specify "no solvent" in `Reaction.from_*()`

Issue - State: closed - Opened by kalekundert almost 5 years ago - 1 comment

#9 - Implement `edit` command

Issue - State: closed - Opened by kalekundert almost 5 years ago

#7 - Support footnote references like [1,2] or [1-3]

Issue - State: closed - Opened by kalekundert almost 5 years ago - 1 comment

#6 - Handle PDF protocols

Issue - State: closed - Opened by kalekundert almost 5 years ago

#5 - Think about renaming `lpr`

Issue - State: closed - Opened by kalekundert almost 5 years ago - 1 comment

#4 - Add option to hide footnotes.

Issue - State: closed - Opened by kalekundert almost 5 years ago - 1 comment

#3 - Ignore __init__.py when loading protocols.

Issue - State: closed - Opened by kalekundert almost 5 years ago

#2 - Specify minimum volume for any reagent in master mix

Issue - State: closed - Opened by kalekundert almost 5 years ago

#1 - Gracefully handle protocols that don't match file format

Issue - State: closed - Opened by kalekundert almost 5 years ago