What’s new in 0.3#

0.3 is the first public version of Ingence, so there is no earlier public release to compare it with. This page lists what Ingence does in it, in the order you meet it. If you have used a development build, Upgrading a project says what happens to your projects.

It opens itself#

Type ingence see with nothing after it. A page opens in your browser. With no project yet, it first asks for the folder to read, a name and where the project goes. Then it asks only what the engine needs before a first reading (the years a date in a name may fall in, whether to open files as well as read their names, and who is deciding), and reads your folder when you click “Read it now”, showing what it has seen so far. The same steps, one command each, are ingence init, ingence index, ingence dive and ingence infer (Your first project).

Your work laid out by time#

The Dashboard opens on the Years view: your experiments by date, at every scale from the whole project down to a single file. Where each member of a laboratory has a folder, the first view has one row per person. Experiments that share words in their names are drawn together as lines of work, and you can give a line a name of your own. Each mark is colored by how much of its raw data was followed by an analysis. Two more views, the Wheel and Overlap, show the same lines as rings and show how steady each one is and which words two lines share.

The No analysis found page lists experiments that have raw data and little or no analysis among the files read: at least five raw acquisitions found, fewer than half followed by an analysis, and fewer than five analysis files and three results tables of the experiment’s own (four settings), each with a reason where one can be given. It says “found”, never “does not exist”, and you can say where an analysis is. The Inventory page counts what is there by kind, and what could not be settled beside what could. Search finds experiments, analysis folders and finished figures by a word, a technique, a condition or a date, and says why each result matched.

Questions come as a sheet#

The Questions page opens on the sheet: the questions that settle the most at once, one card for each class of files, pairs or words, each saying what answering it settles. The older sections stay beside it: Questions (what no rule could decide), Groupings, Claim samples, Proposed pairs, Extensions, Programs and Coverage.

Nothing changes under you. What an answer, a word’s meaning, a pack or a setting does to Ingence’s conclusions waits for Re-run, behind a count of what is waiting. While it works, the pages keep showing the last finished run. Two things show at once: a question you answered leaves the list of open questions, and a name you give a line of work appears. Each answer is added to a log under your name and never overwrites an earlier one. The History page shows, in sentences, what changed between two runs, and a run can be restored after a preview.

Words and packs#

Names are read more closely. A plural is read as the word it comes from, two known words written together are divided, and a phrase of several words can be one meaning. Eight domain packs ship, and a pack is loaded without a question where your files are in a format that declares it (Nikon’s ND2 files for the microscopy pack).

A laboratory can carry its own words: ingence teach export-answers writes what a project was taught as a pack, and ingence teach pack install installs a pack from a file, a folder or a web address (Writing a pack).

What it works out#

  • Which folders are experiments, from their contents and from a date in their name.

  • Stages, raw, processed and analysis, from names, formats and what was made from what.

  • Replicates, and files that are copies of one another by their contents.

  • Files that seem made from other files, proposed to you as pairs, never asserted.

  • Groups of experiments that share words, proposed from several experiments and approved by you.

  • Programs installed inside data folders, set aside so they do not read as experiments.

  • Links that point at nothing, and folders that have moved.

  • A public archive’s list of files, read as if it were a folder, without downloading the files (Public archives).

Care with someone else’s folder#

ingence init --depth metadata makes “open no file” a project’s default, so a plain ingence dive there opens nothing and says so. It is a default and not a lock: ingence dive --depth standard or ingence dive --depth deep still opens files, and anyone using the project can run it. ingence index --dry-run reports what a census would find and writes nothing. A project can live anywhere, and links are never followed out of the folder being read (Read someone else’s folder). Reading the stored names again, inferring, answering questions and the Dashboard’s pages work with the drive unplugged. A new census or a dive needs it.

The rules, in plain words#

ingence rule show prints every rule in force as English. The Engine page shows each rule with how much of a run rests on it, the Dictionary, and every setting with its purpose. The reference pages are generated from the code, so they say only what the engine does.

What is not in 0.3#

  • A held-out measurement on real laboratories. How Ingence is checked, and what that does not show, is on What the evaluation says.

  • A report for problems with the names removed. ingence teach shapes prints the shapes of your names without the names (Reporting a problem).

  • A de-identified export of the graphs Ingence builds (Science).

  • A guide to reading each view of the Dashboard. Not written yet.

  • Every rule. Some rules in the shipped Rulebook are declared and not yet built to run. ingence infer says how many, and --verbose lists them.

  • Settled interfaces. The set of commands is settled; their options are not.