Visualizing relationships between python packages

Save to wide-silo-135723:github_clustering.packages_in_file_py:

SELECT
  id,
  NEST(UNIQUE(COALESCE(
      REGEXP_EXTRACT(line, r"^from ([a-zA-Z0-9_-]+).*import"),
      REGEXP_EXTRACT(line, r"^import ([a-zA-Z0-9_-]+)")))) AS package
FROM (
  SELECT
    id AS id,
    LTRIM(SPLIT(content, "\n")) AS line,
  FROM
    [fh-bigquery:github_extracts.contents_py]
  HAVING
    line CONTAINS "import")
GROUP BY id
HAVING LENGTH(package) > 0;

Table will have two fields – id representing the file and repeated field with packages in the single file. Repeated fields are like arrays – the best description of repeated fields I found.

This is the only step that is specific for python.

Check that imports have been correctly parsed out from some random file.

SELECT
    GROUP_CONCAT(package, ", ") AS packages,
    COUNT(package) AS count
FROM [wide-silo-135723:github_clustering.packages_in_file_py]
WHERE id == "009e3877f01393ae7a4e495015c0e73b5aa48ea7"

packages	count
distutils, itertools, numpy, decimal, pandas, csv, warnings, future, IPython, math, locale, sys	12

SELECT
  COUNT(DISTINCT(package))
FROM (SELECT
  package,
  count(id) AS count
FROM [wide-silo-135723:github_clustering.packages_in_file_py]
GROUP BY 1)
WHERE count > 200;

There are 3501 packages with at least 200 occurrences and it seems like a fine cut off point. Create a filtered table, wide-silo-135723:github_clustering.packages_in_file_top_py:

SELECT
    id,
    NEST(package) AS package
FROM (SELECT
        package,
        count(id) AS count,
        NEST(id) AS id
    FROM [wide-silo-135723:github_clustering.packages_in_file_py]
    GROUP BY 1)
WHERE count > 200
GROUP BY id;

Results are in [wide-silo-135723:github_clustering.packages_in_file_top_py].

SELECT
    COUNT(DISTINCT(package))
FROM [wide-silo-135723:github_clustering.packages_in_file_top_py];

3501

I will generate edges and save it to table wide-silo-135723:github_clustering.packages_in_file_edges_py.

SELECT
  p1.package AS package1,
  p2.package AS package2,
  COUNT(*) AS count
FROM (SELECT
  id,
  package
FROM FLATTEN([wide-silo-135723:github_clustering.packages_in_file_top_py], package)) AS p1
JOIN 
(SELECT
  id,
  package
FROM [wide-silo-135723:github_clustering.packages_in_file_top_py]) AS p2
ON (p1.id == p2.id)
GROUP BY 1,2
ORDER BY count DESC;

Top 10 edges:

SELECT
    package1,
    package2,
    count AS count
FROM [wide-silo-135723:github_clustering.packages_in_file_edges_py]
WHERE package1 < package2
ORDER BY count DESC
LIMIT 10;

package1	package2	count
os	sys	393311
os	re	156765
os	time	156320
logging	os	134478
sys	time	133396
re	sys	122375
__future__	django	119335
__future__	os	109319
os	subprocess	106862
datetime	django	94111

Quantiles of the edge weight:

SELECT
    GROUP_CONCAT(STRING(QUANTILES(count, 11)), ", ")
FROM [wide-silo-135723:github_clustering.packages_in_file_edges_py];

1, 1, 1, 2, 3, 4, 7, 12, 24, 70, 1005020

In my first implementation I filtered edges out based on the total count. It was not a good approach, as a small relationship between two big packages was more likely to stay than strong relationship between too small packages.

Create wide-silo-135723:github_clustering.packages_in_file_nodes_py:

SELECT
  package AS package,
  COUNT(id) AS count
FROM [github_clustering.packages_in_file_top_py]
GROUP BY 1;

package	count
os	1005020
sys	784379
django	618941
__future__	445335
time	359073
re	349309

Create table packages_in_file_edges_top_py:

SELECT
    edges.package1 AS package1,
    edges.package2 AS package2,
    edges.count / IF(nodes1.count  0.33
AND package1 <= package2;

Full results in google docs.

import pandas as pd
import math

df = pd.read_csv(“edges.csv”)
pd_df = df[( df.package1 == “pandas” ) | ( df.package2 == “pandas” )]
pd_df.loc[pd_df.package1 == “pandas”,”other_package”] = pd_df[pd_df.package1 == “pandas”].package2
pd_df.loc[pd_df.package2 == “pandas”,”other_package”] = pd_df[pd_df.package2 == “pandas”].package1

df_to_org(pd_df.loc[:,[“other_package”, “count”]])

print “\n”, len(pd_df), “total edges with pandas”

other_package	count
pandas	33846
numpy	21813
statsmodels	1355
seaborn	1164
zipline	684
11 more rows

16 total edges with pandas

nodes_df = df[df.package1 == df.package2].reset_index().loc[:, [“package1”, “count”]].copy()
nodes_df[“label”] = nodes_df.package1
nodes_df[“id”] = nodes_df.index
nodes_df[“r”] = (nodes_df[“count”] / nodes_df[“count”].min()).apply(math.sqrt) + 5
nodes_df[“count”].apply(lambda s: str(s) + ” total usages\n”)
df_to_org(nodes_df)

package1	count	label	id	r
os	1005020	os	0	75.711381704
sys	784379	sys	1	67.4690570169
django	618941	django	2	60.4915169887
__future__	445335	__future__	3	52.0701286903
time	359073	time	4	47.2662138808
3460 more rows

id_map = nodes_df.reset_index().set_index(“package1”).to_dict()[“index”]

print pd.Series(id_map).sort_values()[:5]

os            0
sys           1
django        2
__future__    3
time          4
dtype: int64

edges_df = df.copy()
edges_df[“source”] = edges_df.package1.apply(lambda p: id_map[p])
edges_df[“target”] = edges_df.package2.apply(lambda p: id_map[p])
edges_df = edges_df.merge(nodes_df[[“id”, “count”]], left_on=”source”, right_on=”id”, how=”left”)
edges_df = edges_df.merge(nodes_df[[“id”, “count”]], left_on=”target”, right_on=”id”, how=”left”)
df_to_org(edges_df)

print “\ndf and edges_df should be the same length: “, len(df), len(edges_df)

package1	package2	strength	count_x	source	target	id_x	count_y	id_y	count
os	os	1.0	1005020	0	0	0	1005020	0	1005020
sys	sys	1.0	784379	1	1	1	784379	1	784379
django	django	1.0	618941	2	2	2	618941	2	618941
__future__	__future__	1.0	445335	3	3	3	445335	3	445335
os	sys	0.501429793505	393311	0	1	0	1005020	1	784379
11117 more rows

df and edges_df should be the same length: 11122 11122

edges_rev_df = edges_df.copy()
edges_rev_df.loc[:,[“source”, “target”]] = edges_rev_df.loc[:,[“target”, “source”]].values
edges_df = edges_df.append(edges_rev_df)
df_to_org(edges_df)

package1	package2	strength	count_x	source	target	id_x	count_y	id_y	count
os	os	1.0	1005020	0	0	0	1005020	0	1005020
sys	sys	1.0	784379	1	1	1	784379	1	784379
django	django	1.0	618941	2	2	2	618941	2	618941
__future__	__future__	1.0	445335	3	3	3	445335	3	445335
os	sys	0.501429793505	393311	0	1	0	1005020	1	784379
22239 more rows

edges_df = edges_df[[“source”, “target”, “strength”]]
df_to_org(edges_df)

source	target	strength
0.0	0.0	1.0
1.0	1.0	1.0
2.0	2.0	1.0
3.0	3.0	1.0
0.0	1.0	0.501429793505
22239 more rows

The whole simulation takes a minute to stabilize. I could just download an image, but there are extra features like pressing the node opens pypi.

Download all positions after the simulation from the javascript console:

var positions = nodes.map(function bar (n) { return [n.id, n.x, n.y]; })
JSON.stringify()

According to d3 documentation, by setting parameter “fx” and “fy” of node we will set it’s fixed position.

pos_df = pd.read_json(“fixed-positions.json”)
pos_df.columns = [“id”, “x”, “y”]
nodes_df = nodes_df.merge(pos_df, on=”id”)

# c will be collision strength
nodes_df[“c”] = pd.DataFrame([nodes_df.label.str.len() * 1.8, nodes_df.r]).max() + 5
nodes_df = nodes_df[[“id”, “r”, “label”, “c”, “x”, “y”]]
df_to_org(nodes_df)

id	r	label	c	x	y
0	75.711381704	os	80.711381704	158.70817237	396.074393369
1	67.4690570169	sys	72.4690570169	362.371142521	-292.138913114
2	60.4915169887	django	65.4915169887	526.471326062	1607.83507287
3	52.0701286903	__future__	57.0701286903	1354.91212894	680.325432179
4	47.2662138808	time	52.2662138808	419.407448663	439.872927665
3460 more rows

# Truncate columns
with open(“graph.js”, “w”) as f:
f.write(“var nodes = {}\n\n”.format(nodes_df.to_dict(orient=”records”)))
f.write(“var nodeIds = {}\n”.format(id_map))
f.write(“var links = {}\n\n”.format(edges_df.to_dict(orient=”records”)))

Simulation uses the new velocity Verlet integration force graph in d3 v 4.0. Simulation takes about one minute to stabilize, so for viewing purposes I hard-coded the position of node after running simulation on my machine.

To re-run the simulation you can:

• Remove fixed positions added in one of pandas processing steps.
• Uncomment the “forces” in the javascript file.

I have been tweaking simulation parameters for a while. Very dense “center” of the graph is in conflict with clusters on the edge of the graph.

As you may see in the current graph, nodes in the center sometimes overlap, while distance between nodes on the edge of a graph is big.

I got as much as I could from the collision parameter and increasing it further wasn’t helpful. Potentially I could increase gravity towards the center, but then some of the valuable “clusters” from edges of the graph got lumped into the big “kernel” in the center. The most promising approach at this point would be to try some ways of Reduce an effect of a heavy weight center cluster.