As the name would suggest, this module allows computing timeline
PageRank on a graph. See documentation in the module for details on the
algorithm.
Test plan: The module has incomplete testing. The timelinePagerank
function calls out to iterators for getting the time-decayed node
weights and the time-decayed markov chain; these iterators are tested.
However, the wrapper logic that composes these pieces together,
calculates seed vectors, and runs PageRank is not tested. I felt it
would be a pain to test and settled for reviewing the code carefully,
and putting a cautionary note at the top of the function.
This commit adds new weight evaluators for nodes and edges. Unlike the
previous evaluator, edges and nodes are handled as separate concerns,
rather than composing the node weights into the edge weights. I think
this separation is cleaner.
Both evaluators use only the address, not the full (Node or Edge)
object. Although we may want to give the edge evaluator access to the
full Edge later, if we decide we want node-type-differentiated edge
weights (e.g. if a hasParent edge has a different weight depending on
whether it is connected to an Issue or a Repository).
weightsToEdgeEvaluator has been refactored to use the new evaluators,
and has been given a deprecation notice.
Test plan: `yarn test`
This commit adds an `interval` module which defines intervals (time
ranges), and methods for slicing up a graph into its consistuent time
intervals. This is pre-requisite work for #862.
I've added a dep on d3-array.
Test plan: Unit tests added; run `yarn test`
#1167 added some info to the README about how the user needs to have ssh keys setup. This was true at the time, but changed as a result of #1210. This commit fixes that up by removing the now-outdated information.
* Quicker failure and description when invalid token supplied
Fixes#1156
When users export a GitHub API token that has insufficient privleges
or has been revoked, we have been using a catch all error with retry
to handle it. This change adds a new error type for bad credentials
and does not retry.
Test plan:
There are no unit tests that cover this, however, you can test the
change by supplying a revoked token and attempting to load a GitHub
repo.
* Minor: reunite comment with relevant code block
* Update Changelog: Fail quicker and with information when using invalid GH token (#1161)
* Documentation updates
Added note on Changelog update format, SSH key requirements, and formatted the console (CLI) blocks a little better.
* Minor formatting fixes
* Revert a line wrap commit as it is not appropriate on README.md
* Removed prompt tokens and changed non-visible formatting
This commit disables the Git plugin by removing it from the default list
of plugins to load, or to display in the frontend.
Rationale: The git plugin doesn't currently add very much to cred
quality. Git commits have edges to their parent, which isn't a very
meaningful relationship for cred purposes. We'll want to re-enable the
Git plugin once we're ready to support e.g. file and directory level
cred tracking.
I've skipped a block of tests around the git analysisAdapter. (I intend
to deprecate the analysisAdapters, so skipping the tests seemed
preferrable to updating them). I also updated our sharness test for
catching test files without a proper describe block, so that it won't
error on skipped blocks.
Test plan: `yarn test --full` passes. Loading a new repository and
inspecting it in the frontend gives consistent results. There are no
references to Git plugin weights in the frontend, now that corresponding
nodes are not available.
The dependabot bot has an inconsistent typename in GitHub's database.
We'll blacklist it so we can continue loading `sourcecred/sourcecred`.
Test plan: `node bin/sourcecred.js load sourcecred/sourcecred` fails
before this commit, and succeeds after.
This commit resolves an inconsistency where we called edge weights
`toWeight` and `froWeight` in the core/attribution module, but
`forwards` and `backwards` in the analysis module.
I changed field names in the PagerankGraph JSON, so I bumped its compat.
Test plan: `yarn test --full` passes.
This commit changes CI to test against node 12 and 10 instead of node 8.
I test against node 12 by default (it will be LTS soon, and it has a
number of nice improvements compared to 10). We test node10 on the
nightly and post-merge, that way we will still discover quickly if we
have a problem with node 10, but it won't slow down CI for merges.
I'm just dropping explicit support for node 8 entirely, since node 8 is
end-of-life soon (Dec 19).
Test plan: I've locally verified that `yarn test --full` passes for both
node 10 and node 12.
This commit just adds a test which verifies that when an
OrderedSparseMarkovChain is created by graphToMarkovChain, its nodeOrder
is the graph's canonical node order.
Test plan: `yarn test`
This means that we no longer need to expose methods for extracting the
order from serialized JSON. We can always count on iterating over the
nodes and edges in sorted order.
Test plan: `yarn test`; tests updated.
I've regenerated the yarn.lock file (by removing it and then re-running
yarn). This picks up [a fix I authored][fix] for node-eval, which was
preventing `yarn test --full` from passing in node 10 and 12. With this
upgrde of transitive dependencies, we're now ready to officially support
newer versions of node.
Test plan: `yarn test` passes.
Since upgrading to flow 0.102.0, we've been having CI issues where flow
fails as "out of retries". In my testing, downgrading flow seems to
resolve this, although it's hard to be certain as the issue strikes
sporadically.
Test plan: This commit definitely works locally; hopefully it will
consistently pass in CI as well.
This commit enables Greenkeeper, along with an initial upgrade push for our dependencies.
I've reverted a number of upgrades, and also added them to the
greenkeeper ignore list. They mostly relate to babel/webpack stuff,
which I'm reluctant to dive into now (there have been major upgrades for
both babel and webpack) but we should address eventually. There are also
a few oddballs like whatwg-fetch and history.
Test plan: `yarn test --full` passes.
This commit updates eslint from v4 to v6. In doing so, I've moved off of
the create-react-app base eslint config. We were on an old version (v2)
and it doesn't make sense to update to v4, as in v4 create-react-app
uses typescript. Also, it didn't make sense to stay on
create-react-app's v2 config, because then it had unmet peer dependency
constraints on old versions of eslint.
Instead, I've moved us to use the default rules for eslint,
eslint-plugin-react, and eslint-plugin-flowtype.
I also made some changes to the codebase to satisfy the new lint rules
that came with this change.
Test plan: `yarn test` passes.
This commit deletes and regenerates the `yarn.lock` file, with the
effect that all dependencies are upaded to the latest version allowed by
our package.json. (For example, if we are pinned to `^2.4.0`, we might
now get `2.6.3`.)
This commit was generated via:
```Bash
$ rm yarn.lock
$ yarn
```
Test plan: `yarn test --full` passes, and I also manually tested the
frontend.
This necessitated a number of type fixes:
- Upgraded the express flow-typed file to latest
- Added manual flow error suppression to where the express flow-typed
file is still using a deprecated utility type
- Removed type polymorphism support on map.merge (see context here[1]).
We weren't using the polymorphism anywhere so I figured it was simplest
to just remove it.
- Improve typing around jest mocks throughout the codebase.
Test plan: `yarn test --full` passes.
[1]: https://github.com/flow-typed/flow-typed/issues/2991
This commit updates our prettier version from `1.13` to `1.18`. Looks
like software does get better over time! I like all of the changes.
Test plan: `yarn test` passes. I've manually inspected the diffs.
When we took a dep on better-sqlite3 in #836, we used a fork, because
better-sqlite3 did not yet support private in-memory databases via the
`:memory:` filepath. As of better-sqlite3 v5, this has been added to
mainline, so we no longer need the fork.
The v4->v5 transition involves some breaking changes. The only ones that
affected us were two field renames, from `lastUpdateROWID` to
`lastUpdateRowid`, and `returnsData` to `reader`.
Test plan:
After updating the field accesses, `yarn test --full` passes. For added
safety, I also blew away cache, loaded a nontrivial repository, and
verified that the full cred workflow still works.
cc @wchargin
Summary:
General cleanup to `update_snapshots.sh`, primarily such that it is free
of race conditions and does not clobber your build output directory. The
mechanism is the same as used in `yarn test`, via `SOURCECRED_BIN`.
Test Plan:
Remove your build directories (`rm -r ./bin ./build`), then run this
script (`./scripts/update_snapshots.sh`) and check that each subprocess
is properly invoked and all tests pass. Check that the temporary build
directory is cleaned up.
wchargin-branch: update-snapshots-cleanup
This updates the graph `Node` type to include a string description.
The description should be a brief (ideally oneline) string giving
context on what the node is. All planned frontends will support
markdown, so linking to context (e.g. linking to the issue corresponding
to an ISSUE type node) is supported.
This commit updates the Git and GitHub plugins to use the new
description field.
Test plan: `yarn test --full` passes, and I've inspected snapshots and
made sure they look reasonable.
The GitHub plugin no longer adds a Node to the graph for Git commits.
Instead, it creates a dangling edge to it. This frees the GitHub plugin
from responsibility for setting the timestamp or other metadata for Git
nodes.
The Git plugin no longer adds a Commit Node to the graph immediately when
encountering a commit's parent hash. Instead, it creates an edge to the
parent, and then fills in the parent node once it is encountered in the
commit store.
Test plan: Load a real repository with merged pull requests
(e.g. sourcecred/research) into the explorer, and verify that GitHub
commit entities are still connected to Git commits, and that Git
commits are still connected to their parents.
This commit modifies the Graph class so that it permits dangling edges;
that is to say, edges whose src or dst are not present in the graph.
Dangling edges may be directly added to the graph, or existing edges may
become dangling if their src or dst is removed.
This change is prerequisite to #1136; if we require that nodes have
metadata, we should also make it possible to add edges to nodes that
don't yet exist, as the plugin creating an edge may not have access to
the full metadata needed to add the node.
To support this change, there is now an `isDanglingEdge` method on the
graph, which reports whether or not the edge is dangling. Also,
`Graph.edges` requires that the client make an explicit choice on
whether dangling edges are desired. This ensures that we do not
accidentally include dangling edges in a case where they are
inappropriate (e.g. creating a Markov chain) or accidentally discard
dangling edges when they are needed (e.g. when merging or serializing).
The Graph's invariant checker has been updated to reflect the new
semantics.
The Graph compat version has been bumped, since this is a break in
backwards compatibility.
Note that this commit does not change the behavior of any plugins; that
is to say, no plugins create dangling edges (yet).
Test plan: The advanced graph test case has been updated to include
dangling edges. The tests for Graph, PagerankGraph, and
GraphToMarkovChain have been updated. `yarn test --full` passes.
This commit modifies the base `Graph` class so that nodes are now
represented by `Node` objects rather than `NodeAddressT`. The intention
is to start adding additional fields (e.g. description and timestamp) to
nodes, although that is not included in this commit.
See #1136 for rationale.
Test plan: The graph is very well tested, and this commit adds
additional tests and invariant checking. Some additional test code
needed update. `yarn test --full` passes, and the SourceCred UI works as
expected.
PagerankGraph's `node` and `edge` getters returned null for unavailable
entries, rather than undefined. This is inconsistent with general JS
behavior, and with the base Graph. I've now cleaned it up.
Test plan: unit tests updated; `yarn test` passes.
Every GitHub entity now has a `description` method which returns a short
markdown description. These will be added to the graph as part of #1136.
Test plan: Inspected snapshots, `yarn test --full`.
This will allow timeline cred (#862) to do a better job of flowing cred
across reaction edges. (Very old reactions should not be moving a lot of
present-day cred.)
Test plan: Inspected snapshot changes.
Every GitHub entity from `RelationalView` now has a `timestampMs`
method. This replaces the standalone `createdAt` method.
Test plan: Snapshots look good.
It's an extension of #1152 induced by #1175.
It's a very simple change; I just changed the schema, and
`scripts/update_snapshots.sh` took care of the rest.
Test plan: Inspected snapshots and generated flow types.
This pulls distribution related code out of `markovChain.js` into the new
`distribution.js` module, and from `graphToMarkovChain.js` into
`nodeDistribution.js`.
Since the `computeDelta` method is now exported, I've added some unit
tests.
Test plan: `yarn test` passes.
As #1136 will be moving timestamps into the graph, we no longer need
`createdAt` method in the `AnalysisAdapter`. Actually, we no longer need
the adapter/loader distinction introduced in #1157. I haven't taken the
time to remove the `BackendAdapterLoader` concept because a) we may need
it later, and b) if we don't, I'll likely remove the `AnalysisAdapter`
concept entirely, in favor of having plugins directly save `graph.json`
files to a known location.
Test plan: `yarn test` passes.
I added `mentionsAuthorReference` based on an untested hypothesis that
they would be useful. With the passage of time, I've never seen any
evidence that they actually improve cred socres (their impact seems
negligible), and they add complexity.
In the future, "go-fishing" style heuristics like this should not merge
unless they are of clearly demonstrated value. Also, it would be better
to add stuff like this via a standalone plugin rather than in the core
GitHub logic.
Undoes #806.
Test plan: `yarn test`
Now that the graph is saved by default as a part of load, users who need
the graph can grab it directly from the `$SOURCECRED_DIRECTORY`. If we
really need a command line util for grabbing it, we should rewrite that
command to just grab the graph from that spot rather than re-computing
it.
Test plan: `yarn test`
As of the timeline cred work, I'm shifting emphasis away from raw
PageRank results, in favor of timeline pagerank results. As such,
there's no need to have load save the regular pagerank results on
creation.
As of #1136, there will be no need for timestampMap, as that data will
be present directly in the graph. As the timeline cred UI will depend on
the full graph for analysis, let's save the graph instead.
Test plan: `yarn test` and snapshot inspection.
This commit adds new helper methods for creating test nodes (`node` and
`partsNode`) and for creating test edges (`edge` and `partsEdge`) to
graphTestUtil.js.
This is very helpful in light of work related to #1136. I'm going to
change the concept of "node" from a raw address to an object, add fields
to that object, and add fields to the `Edge` type. If done naively, we
would need to change all the test code across the project for every one
of those changes.
By centralizing the creation of test nodes and edges behind the new
functions, we can update all the test code in a single place.
This change is trivial from a conceputal perspective, and very
broad-reaching from a code-touching perspective. It should be easy to
review, because if tests pass then the change is probably working as
intended. :)
Test plan: `yarn test`
In #1132 and #1134, I started work on the Odyssey plugin. However,
before getting it to a state where it's usefully included in SourceCred,
I decided to pivot to focus on timeline cred first.
Now I'm merging significant refactors as a part of timeline cred
(#1136). As a side effect of this refactor, the Odyssey plugin should
undergo significant changes (OdysseyInstance is now basically redundant
with base Graph.) Rather than incrementally update unused code, I elect
to remove the plugin. This code should be revived on a side branch, and
then merged into master once we have a fully functioning prototype.
Test plan: `yarn test` passes.
This commit refactors the Graph class so that rather than having
separate maps for inEdges and outEdges, there is a single incidentEdges
map, which contains objects with inEdges and outEdges.
This is motivated by a forthcoming big change as part of #1136; namely, to
allow storing dangling edges in the graph. Once we do so, we'll need a
consistent source of truth that enumerates all of the node addresses
which are accessible in the graph (either because they correspond to a
node in the graph, or because they are the src or dst of a dangling
edge). We could do this by adding another field to graph which tracks
this set, but by making this refactor, we can instead use the key set of
_incidentEdges as the source of truth for which node addresses are
present.
Besides being motivated by #1136, I think it's cleaner in general. Note
there are fewer ways for the graph to be inconsistent, as it's no longer
possible for inEdges and outEdges to have inconsistent sets of node
addresses.
The most complicated piece of this change was updating the automatic
invariant checker. It was no longer possible to test 3.1 and 4.1
separately, so they needed to be merged into a new invariant. Rather
than re-enumerate the invariants, I called the new one the 'Temporary
Invariant', because it is going to disappear in a subsequent commit.
Test plan: `yarn test` passes. Since Graph has extremely thorough
testing, this gives me great confidence in this commit. Note that no
observable behavior has changed.
The generated GitHub GraphQL flow types are a kind of snapshot, and it
can be hard to remember/discover how to update them when making changes
to schema. Therefore, I've included them in the snapshot update script.
Test plan: I used it to update the types, and it worked as intended.
At present, the Git commit node type lives in a strange state of shared
responsibility between GitHub and Git. The Git plugin is nominally
responsible for it, but its render method tries to show a hyperlink to
GitHub -- which is awkward for many reasons, including that the same Git
commit could have multiple hyperlinks on GitHub.
This commit resolves that issue by separating the existing commit type
into two: the Git Commit type, which is owned by the Git plugin and
doesn't have hyperlinks or any fancy GitHub metadata, and the GitHub
Commit, which is owned by the GitHub plugin, corresponds to a unique
database id in GitHub, and has a corresponding GitHub url.
The two commits are connected by a CorrespondsToCommit edge type, which
links from the GitHub commit to the corresponding Git commit.
This is necessary for #1136, as if we want to make descriptions a part
of the graph payload, we need for descriptions to be unique for a given
address--and descriptions are only unique if we identifiy each GitHub
commit pointer as a separate address.
Test plan: The unit testing in this part of the codebase is light, so I
verified that the frontend work as expected for `sourcecred/sourcecred`
and `sourcecred/research`. The new node type and edge type appear
properly in the UI, the GitHub commits are connected to their Git
counterparts, etc.
A long time ago, we made graph views for git and github. These are
interfaces over the graph which allow retrieving nodes' relations, e.g.
finding the parent address of a commit just using the graph.
These are fairly complex, and have seen almost no use at all. The one
thing they are used for is implementing invariant checking. The
invariant checking is nice in principle, but since we only apply it to
the example data, its of very limited value in practice.
Since I'm planning a significant Graph refactor (#1136), I'd rather delete this
code than continue to maintain it, since I think it's complexity/value
ratio is unfavorable.
Test plan: `yarn test`
This is another minor silent test failure: the error message thrown by
loadIndividualPlugin when a GitHub token is not available is not quite
the error that was specified in the test.
There were two issues: that we were testing for the wrong error message,
and that the failure didn't fail the test. I fixed both issues (by
changing the message thrown to match the test, and by having the test
_return_ the expectation that the promise will reject, and by expecting
there to be one assertion.)
Test plan: `yarn unit cli/load` no longer shows any unhandled promise
rejection warnings. If the test is modified so that it checks for the
wrong string, it now properly fails rather than passing with an
unhandled rejection.
Prior to this commit, if you run `yarn unit cli/load`,
you would see a lot of unhandled promise rejection warnings related to
the fact that load calls a `saveTimestamps` function which expects the
SourceCred directory to contain the results of really loading SourceCred
plugins. However, when testing, these functions have been mocked, and so
saveTimestamps rejects. This rejection was not caught, and polluted the
test output without actually failing the tests.
This commit updates the tests so that saveTimestamps can be mocked (via
dependency injection) and we can both verify that it is invoked
correctly, and not pollute the test output with spurious warnings.
Test plan:
- `yarn test --full` passes
- `yarn unit cli/load` produces far fewer
UnhandledPromiseRejectionWarnings (there is still one unrelated one)
- loading sourcecred/research still works (as a canary)
Note: the PR which introduced this issue is #1162.
Dandelion Mané
dependabot[bot]
Tyler Mace
greenkeeper[bot]
William Chargin
dependabot[bot]