可视化 Python 包之间的关系

发布于 2024-10-10 00:42:23 字数 28826 浏览 10 评论 0

我使用了 BigQuery 上的 github 数据，提取 github repo 上的前 3500 个 python 包的共同出现关系。通过速度 verlet 整合的 d3 中的力导向图实现了可视化。我还使用 python-igraph 中的算法聚类了图，并且将其更新到 http://graphistry.com/ 。

参见 d3 可视化中的集群的截图（点击图片以获得在线版本）：

下面是刚刚从 graphistry 提取的 numpy 集群（点击图片以获得在线版本）：

图形属性：

每一个节点是在 github 上找到的一个 python 包。在 DataFrame with nodes 部分计算得到半径。
对于两个包 A 和 B，边的权重是，其中， $|A cap B|$ 是在相同文件中包 A 和包 B 出现的次数。很快，我会将其迁移到标准化的逐点相互信息，因为有点难用 BigQuery 来计算它。
移除权重小于 0.1 的边。
根据仿真参数，按照速度 verlet 集成来 d3 算法搜索最小能量状态。

你可以访问 http://clustering.kozikow.com?center=numpy 看看我的应用。你可以：

在 URL 中传递不同的包名作为查询参数。
水平和垂直滚动页面。
点击一个节点可以打开 pypi 上对应的页面。注意，并不是所有的包在 pypi 上都有。

有趣的 graphistry 视图在下一节，具体集群分析。

图形可视化除了看着酷以外，往往缺乏可操作的见解。

Types of insights you can use this for:

Find packages you have been not aware of in the close proximity of other packages that you use.
Evaluate different web development frameworks based on size, adoption and library availability (e.g. Flask vs django ).
Find some interesting python use cases, like robotics cluster .

Revision history of this post is on github in the orgmode .

具体集群分析

In addition to d3 visualization I also clustered the data using the python-igraph community_infomap().membership and uploaded it to graphistry. Ability to exclude and filter by clusters was very useful.

科学计算集群

Unsurprisingly, it is centered on numpy. It is interesting that it is possible to see the divide between statistics and machine learning.

Web 框架集群

Web 框架很有意思：

d3 链接

It could be said that sqlalchemy is a center of web frameworks land.
Found nearby, there's a massive and monolithic cluster for django .
Smaller nearby clusters for flask and pyramid .
pylons , lacking a cluster of its own, in between django and sqlalchemy.
Small cluster for zope , also nearby sqlalchemy
tornado got swallowed by the big cluster of standard library in the middle, but is still close to other web frameworks.
Some smaller web frameworks like gluon (web2py) or turbo gears ended up close to django, but barely visible and without clusters of their own.

有趣的 graphistry 集群

其他有趣的集群

Looking at results of clustering algorithm, only "medium sized" clusters are interesting. A few first are obvious like clusters dominated by packages like os and sys. Very small clusters are not interesting either. Here you can see clusters between positions 5 and 30 according to size .

Some of the other clusters:

Testing cluster, d3 link , graphistry cluster
Openstack cluster, d3 link , graphistry link
String parsing and formatting cluster
Robotics land
gaming cluster
deep learning cluster

进一步分析的潜力

其他编程语言

Majority of the code is not specific to python. Only the first step, create a table with packages, is specific to python.

I had to do a lot of work on fitting the parameters in Simulation parameters to make the graph look good enough. I suspect that I would have to do similar fitting to each language, as each language graph would have different properties.

I will be working on analyzing Java and Scala next.

搜索"打包 X 的替代品"，例如，seaborn vs bokeh

For example, it would be interesting to cluster together all python data visualization packages.

Intuitively, such packages would be used in similar context, but would be rarely used together. Assuming that our graph is represented as npmi coincidence matrix M, for packages x and y, correlation of vectors x and y would be high, but M[x][y] would be low.

Alternatively, M^2 /. M could have some potential. M^2 would roughly represent "two hops" in the graph, while /. is a pointwise division. e high correlation of their neighbor weights, but low direct edge.

This would work in many situations, but there are some others it wouldn't handle well. Example case it wouldn't handle well:

sqlalchemy is an alternative to django built-in ORM.
django ORM is only used in django.
django ORM is not well usable in other web frameworks like flask.
other web frameworks make heavy use of flask ORM, but not django built-in ORM.

Therefore, django ORM and sqlalchemy wouldn't have their neighbor weights correlated. I might got some ORM details wrong, as I don't do much web dev.

I also plan to experiment with node2vec or squaring the adjacency matrix.

在 repo 关系中

Currently, I am only looking at imports within the same file. It could be interesting to look at the same graph built using "within same repository" relationship, or systematically compare the "within same repository" and "within same file" relationships.

加入 pypi

It could be interesting to compare usages on github with pypi downloads. Pypi is also accessible on BigQuery .

数据

Post-processed JSON data used by d3
Publicly available BigQuery tables with all the data . See Reproduce section to see how each table was generated.

重现步骤

从 BigQuery 抽取数据

创建一个包表

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.

验证 packages_in_file_py 表

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

过滤掉不常用的包

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];

生成图形的边

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

过滤掉不相关的边

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 the table packages_in_file_edges_top_py:

SELECT
    edges.package1 AS package1,
    edges.package2 AS package2,
    # WordPress gets confused by less than sign after nodes1.count
    edges.count / IF(nodes1.count nodes2.count,
        nodes1.count,
        nodes2.count) AS strength,
    edges.count AS count
FROM [wide-silo-135723:github_clustering.packages_in_file_edges_py] AS edges
JOIN [wide-silo-135723:github_clustering.packages_in_file_nodes_py] AS nodes1
    ON edges.package1 == nodes1.package
JOIN [wide-silo-135723:github_clustering.packages_in_file_nodes_py] AS nodes2
    ON edges.package2 == nodes2.package
HAVING strength > 0.33
AND package1 <= package2;

Full results in google docs.

Process data with Pandas to json

加载 csv，并用 pandas 验证边

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

DataFrame with nodes

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

Create map of node name -> id

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

Create edges data frame

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

Add reversed edge

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

Truncate edges DataFrame

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

After running simulation in the browser, get saved positions

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()

Join the positions x and y with edges dataframe, so they will get picked up by
the d3.

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

Truncate nodes DataFrame

# c will be collision strength. Prevent labels from overlaping.  
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

保存文件到 json

# 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")))

使用新的 d3 速度 verlet 集成算法绘制图

The physical simulation 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.

The core component of the simulation is:

var simulation = d3.forceSimulation(nodes)
  .force("charge", d3.forceManyBody().strength(-400))
  .force("link", d3.forceLink(links).distance(30).strength(function (d) {
      return d.strength * d.strength;
  }))
  .force("collide", d3.forceCollide().radius(function(d) {
      return d.c;
  }).strength(5))
  .force("x", d3.forceX().strength(0.1))
  .force("y", d3.forceY().strength(0.1))
  .on("tick", ticked);

To re-run the simulation you can:

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

仿真参数

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.

Plotting some big clusters separately worked well to solve this problem.