clam | Quickly turn command-line applications | REST library
kandi X-RAY | clam Summary
kandi X-RAY | clam Summary
Quickly turn command-line applications into RESTful webservices with a web-application front-end. You provide a specification of your command line application, its input, output and parameters, and CLAM wraps around your application to form a fully fledged RESTful webservice.
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Top functions reviewed by kandi - BETA
- Parse the CLAM XML document
- Create a new Inputtemplate from an XML node
- Create a profile from an XML node
- Create a constraint from an XML node
- Get a CLAM output file
- Return the path to a project
- Download an archive
- Set default values
- Prints an error message
- Get file from public storage
- Raise an error
- Load configuration file
- Handle GET request
- Generates a program that matches the given parameters
- Tries to create project directories
- Decorator to require authentication
- Create a Parameter object from an XML node
- Calculate statistics for a given file
- Update index
- Delete a project
- Verify the authentication
- Get information about a project
- Add input file to project
- Decorator to require login headers
- Generates an output file for this output template
- Show an admin action
- Get an input file
clam Key Features
clam Examples and Code Snippets
Community Discussions
Trending Discussions on clam
QUESTION
ANSWER
Answered 2022-Mar-20 at 16:38As suggested by @Thingamabobs and @acw1668 It's possible to change the focus color of a ttk.Entry
by mapping the focus state in its style property. Here is the working code:
QUESTION
This was my earlier question where it was solved using multiple distribution.
I want to plot the continuous variable like age or tumor mutation burden as shown in first figure with a range like a window such 20-30 age group or some mutational burden range
The frequencies are calculated for all the variables of the metadata, but when plotting the age is not mapped to the final plot as show in the second plot.
Does the age need to be converted into other class before plotting?
...ANSWER
Answered 2022-Mar-14 at 09:14Rename Diagnosis-Age
and use cut
to convert to a factor. Add labels as required for appearance of age groups in legend.
Note I have swapped name
and perc
in the call to aes
to avoid the call to coord_flip
.
QUESTION
ANSWER
Answered 2022-Mar-06 at 02:42There are two issues in your code:
my_canvas.configure(yscrollcommand=my_scrollbar.set)
should bemy_canvas.configure(xscrollcommand=my_scrollbar.set)
when adding items to
seccond_frame
, it isseccond_frame
get resized, notmy_canvas
. So you need to bindon
seccond_frame
instead ofmy_canvas
QUESTION
ANSWER
Answered 2022-Mar-02 at 12:15library(tidyverse)
library(ggnewscale)
plot_meta <- structure(list(
patient = structure(c(
36L, 33L, 122L, 95L, 66L,
49L
), .Label = c(
"TCGA-AB-2805", "TCGA-AB-2806", "TCGA-AB-2808",
"TCGA-AB-2810", "TCGA-AB-2811", "TCGA-AB-2812", "TCGA-AB-2813",
"TCGA-AB-2814", "TCGA-AB-2815", "TCGA-AB-2817", "TCGA-AB-2818",
"TCGA-AB-2819", "TCGA-AB-2820", "TCGA-AB-2821", "TCGA-AB-2822",
"TCGA-AB-2823", "TCGA-AB-2825", "TCGA-AB-2826", "TCGA-AB-2828",
"TCGA-AB-2830", "TCGA-AB-2834", "TCGA-AB-2835", "TCGA-AB-2836",
"TCGA-AB-2839", "TCGA-AB-2840", "TCGA-AB-2841", "TCGA-AB-2842",
"TCGA-AB-2843", "TCGA-AB-2844", "TCGA-AB-2845", "TCGA-AB-2846",
"TCGA-AB-2847", "TCGA-AB-2849", "TCGA-AB-2851", "TCGA-AB-2853",
"TCGA-AB-2856", "TCGA-AB-2857", "TCGA-AB-2858", "TCGA-AB-2859",
"TCGA-AB-2861", "TCGA-AB-2862", "TCGA-AB-2863", "TCGA-AB-2865",
"TCGA-AB-2866", "TCGA-AB-2867", "TCGA-AB-2869", "TCGA-AB-2870",
"TCGA-AB-2871", "TCGA-AB-2872", "TCGA-AB-2873", "TCGA-AB-2874",
"TCGA-AB-2875", "TCGA-AB-2876", "TCGA-AB-2877", "TCGA-AB-2878",
"TCGA-AB-2880", "TCGA-AB-2881", "TCGA-AB-2882", "TCGA-AB-2883",
"TCGA-AB-2884", "TCGA-AB-2885", "TCGA-AB-2886", "TCGA-AB-2888",
"TCGA-AB-2889", "TCGA-AB-2890", "TCGA-AB-2891", "TCGA-AB-2892",
"TCGA-AB-2893", "TCGA-AB-2894", "TCGA-AB-2895", "TCGA-AB-2896",
"TCGA-AB-2897", "TCGA-AB-2898", "TCGA-AB-2899", "TCGA-AB-2900",
"TCGA-AB-2901", "TCGA-AB-2908", "TCGA-AB-2910", "TCGA-AB-2911",
"TCGA-AB-2912", "TCGA-AB-2913", "TCGA-AB-2914", "TCGA-AB-2915",
"TCGA-AB-2916", "TCGA-AB-2917", "TCGA-AB-2918", "TCGA-AB-2919",
"TCGA-AB-2920", "TCGA-AB-2921", "TCGA-AB-2924", "TCGA-AB-2925",
"TCGA-AB-2927", "TCGA-AB-2928", "TCGA-AB-2929", "TCGA-AB-2930",
"TCGA-AB-2931", "TCGA-AB-2932", "TCGA-AB-2933", "TCGA-AB-2934",
"TCGA-AB-2935", "TCGA-AB-2936", "TCGA-AB-2937", "TCGA-AB-2938",
"TCGA-AB-2939", "TCGA-AB-2940", "TCGA-AB-2941", "TCGA-AB-2942",
"TCGA-AB-2943", "TCGA-AB-2944", "TCGA-AB-2946", "TCGA-AB-2948",
"TCGA-AB-2949", "TCGA-AB-2950", "TCGA-AB-2952", "TCGA-AB-2955",
"TCGA-AB-2956", "TCGA-AB-2959", "TCGA-AB-2963", "TCGA-AB-2965",
"TCGA-AB-2966", "TCGA-AB-2970", "TCGA-AB-2971", "TCGA-AB-2973",
"TCGA-AB-2975", "TCGA-AB-2976", "TCGA-AB-2977", "TCGA-AB-2979",
"TCGA-AB-2980", "TCGA-AB-2981", "TCGA-AB-2982", "TCGA-AB-2983",
"TCGA-AB-2984", "TCGA-AB-2986", "TCGA-AB-2987", "TCGA-AB-2988",
"TCGA-AB-2990", "TCGA-AB-2991", "TCGA-AB-2992", "TCGA-AB-2994",
"TCGA-AB-2995", "TCGA-AB-2996", "TCGA-AB-2998", "TCGA-AB-2999",
"TCGA-AB-3000", "TCGA-AB-3001", "TCGA-AB-3002", "TCGA-AB-3007",
"TCGA-AB-3008", "TCGA-AB-3009", "TCGA-AB-3011", "TCGA-AB-3012"
), class = "factor"), Sex = structure(c(2L, 2L, 1L, 1L, 2L, 2L), .Label = c("Female", "Male"), class = "factor"), FAB = structure(c(
5L,
1L, 5L, 3L, 2L, 4L
), .Label = c(
"M0", "M1", "M2", "M3", "M4",
"M5", "M6", "M7", "nc"
), class = "factor"), `Diagnosis-Age` = c(
63L,
39L, 76L, 62L, 42L, 42L
), `Bone-Marrow-Blast-Percentage` = c(
82L,
83L, 91L, 72L, 68L, 88L
), Cytogenetics = structure(c(
75L, 93L,
51L, 27L, 21L, 57L
), .Label = c(
"37~49,XY,+Y,der(1)add(1)(p13)del(1)(q21q25),-5,der(7)inv(7)(p15q11.2)?inv(7)(q22q32),+17,add(17)(p13),+21,+mar[cp20]",
"39~47,XX,del(5)(q13q33),-7,der(8)t(8;?8;8)(p23;?p11.2p23;q11.2),der(14)t(1;14)(p12;p11.2)der(1)t(7;16)(p15;q22),+2mar[cp19]",
"41~44,X,?i(X)(p10),-7,der(12)t(8;12)(q11.2;p11.2),-8 [cp11]/46,XX[8[",
"42,XY,-5,-7,add(12)(p13),t(14;15)(q10;q10),der(17)t(5;17)(p13;p11.2),-18[6]/40,idem,-11,-add(12)(p13),der(12)t(?;12)(?;p13),-19[6]/41,idem,-der(17)[3]/41,idem,-der(17),+mar1,+mar[3]/41,idem,der(1)der(1)(p12)add(1)(p12),+der(1)(q21)add(1)(q21),-3,-8[2]",
"43,XY-3,del(5)(q12q33),-7,der(10)t(10;11)(q26;q13),-12,-18,+2mar[20]",
"44-45,X,-Y,-5,add(16)(q22),-17,-18,iso(21),+mars[cp5]/82-84,XX,-Y,-3,-4,-11,-12,-19,-21,+21[cp5}",
"44~46,XX,del(11)(q23),der(19)?t(11;19)(q23;p13.1)[cp11]/44~45,XX,-19[cp4]/46,XX [5]",
"44~47,XX,t(1;15)(q32;q26)[14],del(5)(q13q33)[19],-7[20],+8[7],del(12)(p11.2p11.2)[15],del(17)(q21)[8],der(22)t(1;22)(p13;p11.2)[20],+mar[13][cp20]",
"44~47,XY,del(5)(q22q35)[20],-7[14],-8[6],der(12)t(10;12)(p11.2q21)[2],add(14)(p12)[11],-17[13],der(17)t(10;17)(q11.2;p13)[14],-18[7],add(18)(p11.2)[7],-21[10],i(21)(q10)[4],-22[4],+mar[10],+mar1x2[6][cp20]",
"45,X,-X,t(8;21)(q22;q22)[20]", "45,X,-Y, t(8;7;21)(q22;p15;q22[22]/46,XY[3]",
"45,X,-Y,t(8;21)(q22;q22)[13]/45,idem,del(9)(q22;q32)[7]", "45,X,-Y,t(8;21)(q22;q22)[19]/46,XY[1]",
"45,X,-Y[3]/46,XY [17]", "45,XX-7[5]-only 5 metaphases", "45,XX,-7,t(9;11)(p22;q23)[19]/46,XX[1]",
"45,XX,-7[12]/46,XX[8]", "45,XX,-7[20]", "45,XY,-7, t(9;22)(q34;q11.20) [19]/46,XY[1]",
"45,XY,-7[20]", "45,XY,der(7)(t:7;12)(p11.1;p11.2),-12,-13,+mar[19]/46,XY[1]",
"45~46,XY,add(X)(q22)[7],Y[4],der(5)t(5;17)(q13;21)[18],-7[18],+8[17],del(12)(q23)[16],-17[18],add(18)(p11.2)[14][cp18]",
"46, XX[14]", "46, XX[15]", "46, XX[16]", "46, XX[19]", "46, XX[20]",
"46, XY[15]", "46, XY[20]", "46,XX,1~50dmin[12]/46,idem,der(6)t(6;?)(q22;?)[2]/46,XX[6]",
"46,XX,9qh+[20]", "46,XX,del(3)(q23q26.2),der(7)t(1:7)(q32;q32),del(10)(q22q25),t(13;16)(q34;p11.2)dup(21)(q22)[cp20]",
"46,XX,del(5)(q11.2q33)[1]/48~52,idem,+1,+?del(5)(q15q33),+11,+11,?t(12;22)(p13;q12),-13,-17,+i(22)(q10),+i(22)(q10),+mar[cp19]",
"46,XX,del(5)(q22q33)[4]/46,XX[16]", "46,XX,i(17)(q10)[1]/45,sl-7[2]/48,sl,+13,+19[3]/46,XX[15]",
"46,XX,inv(16)(p13q22)[15]/46,XX[2]", "46,XX,inv(16)(p13q22)[19]/46,XX[1]",
"46,XX,inv(16)(p13q22)[20]", "46,XX,inv(16)(p13q22)[5]/46,idem,t(3;3)(p13;q?28)[5]/46,XX[6]",
"46,XX,t(15;17)(q22;q21.1)[19]/47,idem,+8 [1]", "46,XX,t(15;17)(q22;q21),t(16;19)(p13.3;p13.1)[17]/46,XX[3]",
"46,XX,t(15;17)(q22;q21)[11]/46,XX[9]", "46,XX,t(15;17)(q22;q21)[12]/46,XX[8]",
"46,XX,t(15;17)(q22;q21)[20]", "46,XX,t(8;21)(q22;q22)[17]/46,XX[3]",
"46,XX,t(8;21)(q22;q22)[20]", "46,XX,t(8;21)[15]/46,idem,del(9)(q12q22)[5]",
"46,XX[15]", "46,XX[18]", "46,XX[19]/46,XX,add(7)(p?22)[1]",
"46,XX[20]", "46,XX+13,21[cp17]/46,XX[3]", "46,XY,9qh+[19]",
"46,XY,del(11)(p12)[2]/46,XY[18]", "46,XY,del(20)(q11.2)[23]/92,XXYY,del(20)(q11.2)x2[2]/46,XY[3]",
"46,XY,del(7)(q21q36)[18]/46,XY[2]", "46,XY,del(9)(q13:q22),t(11:21)(p13;q22),t(15;17)(q22;q210[20]",
"46,XY,i(17)(q10)[15]/47,XY,idem+13[3]/46,XY[2]", "46,XY,inv(16)(p13;q22)[20]",
"46,XY,inv(16)(p13q22)[17]/46,XY[3]", "46,XY,inv(16)(p13q22)[9]/46,XY[10]",
"46,XY,t(11;19)(q23;p13)[17]/46,XY,t(11;19)(q23;p13),inv(12)(p12p13)[3]",
"46,XY,t(11;19)(q23;p13)[20]", "46,XY,t(15;17)(q22;q21)[19]/46,XY[1]",
"46,XY,t(15;17)(q22;q21)[20]", "46,XY,t(15;17)(q22:q21)[11]/46,XY[9]",
"46,XY,t(2;4)(q34;q21)inv(16)(p13q22) [20]", "46,XY,t(6;11)(q27;q23)[15]",
"46,XY,t(9;11)(p22;q23)[7]/47,XY,t(9;11)(p22;q23)[7]/46,XY[4]",
"46,XY,t(9;22)(q34;q11.2)[13]/34~37,idem,-3,del(4),-4,-5,-7,-9,-10,t?(11;12),-12,-14,-14,-16,-17,-22[cp6]/46,XY[1]",
"46,XY,t(9;22)(q34;q11.2[4]/50,idem,+8,+10,+21,+der(22)(t(9;22)(q34;q11.2)[16]",
"46,XY[13]", "46,XY[15]", "46,XY[19]", "46,XY[20]", "46,XY[30]",
"46~49,XY,del(3)(p14),del(5)(p11.2q33),del(17)(q21q21),add(21)(p11.2),+22,mar[cp20]",
"47,XX,+der(5)t(2;5)(p11.2;q11.2)?,t(8;16)(p11.2;p13.3)[19]",
"47,XX,i(11)(q10)[18]/46,XX [2]", "47,XX,t(15;17)(q22:q21)+mar[20]",
"47,XX+11 [20]", "47,XX+8 [20]", "47,XXY [17]", "47,XY,+13[5]/46,XY[15]",
"47,XY,+21 [6]/46,XY[13]", "47,XY,+21[11]/48,XY,+3,+21[8]", "47,XY,+22[10]/47,XY,+8[7]/45,XY,del(3)(p21),del(4)(p12p15),-7,?dup(7)(q11.2q36)[3]",
"47,XY,+8 [10]/46,XY [10]", "47,XY,+8 [19]", "47,XY,+8 [20]",
"47,XY,+8[15]/46,+8,-17[3]", "47,XY,+9[10]/46,XY[10]", "47,XY,del(5)(q22q33),t(10;11)(p13~p15;q22~23),i(17)(q10)[3]/46,XY[17]",
"47,XY,del(7)(q22),+8,t(15;17)(q22;q21)[18]/46,XY,del(7)(q22),t(15;17)(q22;q21)[2]",
"47,XY+8 [15]/48,XY+8+8[4]/46,XY[1]", "48,XY,+8,+8[16]/46,XY[4]",
"52~54,XY,+2,+4,+6,+8,del(11)(q23),+19,+19,+21[17]/46,XY[3]",
"53~56,XY,+1,del(2)(q33q34),+8,+10,+11x2,+13x1-2,+14,del(17)(p11.2),+19,add(21)(q22),+22[cp20]",
"incomplete-46,XY,del(12)(p11.20[2]/46,XY[3]", "N.D.", "ND",
"Outside hospital with inv(16)"
), class = "factor"), `Cytogenetic-Code--Other-` = structure(c(
8L,
3L, 8L, 8L, 3L, 9L
), .Label = c(
"BCR-ABL1", "CBFB-MYH11", "Complex Cytogenetics",
"Intermediate Risk Cytogenetic Abnormality", "MLL translocation, poor risk",
"MLL translocation, t(9;11)", "N.D.", "Normal Karyotype", "PML-RARA",
"Poor Risk Cytogenetic Abnormality", "RUNX1-RUNX1T1"
), class = "factor"),
Induction = structure(c(11L, 4L, 1L, 8L, 4L, 9L), .Label = c(
"7+3",
"7+3, dauna", "7+3, IT", "7+3+3", "7+3+3, gleevec", "7+3+3, then 5+2+2",
"7+3+3+PSC", "7+3+AMD", "7+3+ATRA", "7+3+dauno", "7+3+Genasense",
"7+3+study drug", "7+4+ATRA", "Azacitidine", "CLAM", "Cytarabine only",
"Decitabine", "Decitabine then 7+3", "Hydrea & Idarubicin",
"Hydrea, ATRA started", "hydrea, didn't get add'l chemo",
"LBH/Decitabine", "low dose Ara C", "no treatment", "Revlimid",
"Revlmd then Decitbne,7+3,5+2"
), class = "factor")
), row.names = c(
NA,
6L
), class = "data.frame")
df <-
plot_meta %>%
mutate(across(everything(), as.character)) %>%
pivot_longer(everything()) %>%
count(name, value) %>%
group_by(name) %>%
mutate(perc = n / sum(n) * 100)
df
#> # A tibble: 38 × 4
#> # Groups: name [8]
#> name value n perc
#>
#> 1 Bone-Marrow-Blast-Percentage 68 1 16.7
#> 2 Bone-Marrow-Blast-Percentage 72 1 16.7
#> 3 Bone-Marrow-Blast-Percentage 82 1 16.7
#> 4 Bone-Marrow-Blast-Percentage 83 1 16.7
#> 5 Bone-Marrow-Blast-Percentage 88 1 16.7
#> 6 Bone-Marrow-Blast-Percentage 91 1 16.7
#> 7 Cytogenetic-Code--Other- Complex Cytogenetics 2 33.3
#> 8 Cytogenetic-Code--Other- Normal Karyotype 3 50
#> 9 Cytogenetic-Code--Other- PML-RARA 1 16.7
#> 10 Cytogenetics 45,XY,der(7)(t:7;12)(p11.1;p11.2),-… 1 16.7
#> # … with 28 more rows
df %>%
ggplot(aes(name, perc)) +
geom_col(data = ~ filter(.x, name == "FAB") %>% rename(FAB = value), mapping = aes(fill = FAB)) +
new_scale_fill() +
geom_col(data = ~ filter(.x, name == "Sex") %>% rename(Sex = value), mapping = aes(fill = Sex)) +
new_scale_fill() +
geom_col(data = ~ filter(.x, name == "Induction") %>% rename(Induction = value), mapping = aes(fill = Induction)) +
coord_flip()
QUESTION
Somehow the buttons placed using grid method will be much bigger than the cell width defined by columnconfigure
. I tried to place some test labels in the same way, and it worked as expected. Is there any way to get correct button width like these labels did?
Below is the simplified code to the question:
...ANSWER
Answered 2022-Feb-16 at 11:28weight
is just a guideline to the layout manager how to distribute available spaces. Since there is no widget in cell (row 1, column 0), it may not get the required space.
It can be enforced by adding uniform=1
to those columnconfigur(...)
:
QUESTION
I am trying to insert a vertical scrollbar in a treeview such that it is displayed under the columns labels of the treeview and not besides/next to the labels. I've tried adding pady in the scrollbar widget yet that still does not place it under the columns labels (just creates an offset from the top). Any help is greatly appreciated (looking at your @Bryan Oakley). I've tried numerous padding techniques to make the vertical scrollbar start below the columns labels yet nothing has worked thus far. Here is a minimal working code:
...ANSWER
Answered 2022-Jan-27 at 04:13You can put the scrollbar at the right side of the cell of tree
:
QUESTION
I am trying to add my GUI and get data from the simple scanner demo application in python. This scanner demo application handles various events like scan event, scanner_connected, scanner_disconnected etc.
Initially I'm calling the GUI class in the demo application to initiate the GUI. When the scan event raises , I take the data and pass the data to a Bridge class. After that I call a GUI function called write_data which is responsible to print the data to a table. This write_table function calls the Bridge class to get the updated scan data
...ANSWER
Answered 2021-Oct-28 at 13:38The write_data function is not indented and is not a method of the class mainGUI. (This was fixed)
You try to access the self.tree variable before it is initialized.
The line where you call self.tree:
QUESTION
I'm trying to make two List
components: one of them is static and small, the second is incredibly large and dynamic. In the first List
I store food categories: Alcoholic products, Soups, Cereals, etc. In the second List
, the word is searched directly from the database - it can be anything: a dish or a category of dishes. Below is the code - it displays the start page. Initially, the first static and small List
is located on it, as well as the Search component (Navigationview.seacrhable()
). When you type a word into the search bar, the first List
disappears and the second one appears. At the moment, both sheets are loaded asynchronously. This is necessary because the second sheet is really big (thousands of rows). This is where my problem begins. Sometimes, when you type a word into the search bar, a copy of this sheet appears on top of it, as shown in the image. It only happens for a fraction of a second, but it's still noticeable. The problem is most likely due to asynchronous loading, before I added it, the List
was loading super slowly, but without such bugs.
My minimal reproducible example:
ContentView.sfiwt
Main List, displaying the food categories available for selection.
...ANSWER
Answered 2021-Nov-19 at 22:27Besides using id
for the IDs, as mentioned in the comments, you can do some refactoring to get SwiftUI to not re-render as much of the view hierarchy and instead reuse components. For example, you have an if
condition and in each you have separate Section
, ForEach
, etc components. Instead, you could render the content of the ForEach
based on the state of the search:
QUESTION
The purpose of the codes is
- For each of three questions (GUI interface with Combobox style), I have to choose one item.
- Each item to the corresponding question represents a set of numbers.
- Based on what I chose for three questions, the codes will calculate the intersection of sets and show the answer on the screen.
Vall, Vcs, V360...are vectors of intergers. Suppose they are given. Ex: Vall = [6,8,13,17,23,38]... Of course, all of vectors are of the same dimension.
Codes:
...ANSWER
Answered 2021-Nov-18 at 15:22The only problem I see is you are dumping the entire function call in the command
argument. That's not how it works. command
should equal a reference to the function you want to call, like this:
command=set_intersection
However, you have a bunch of args that you want to pass. You could make those args global
or you can just wrap the whole thing in a lambda
. One way to do it is like this:
command = lambda r1=recc1, r2=recc2, r3=recc3: set_intersection(r1,r2,r3)
when you do this: command = set_intersection(recc1,recc2,recc3)
you are telling python that command
equals my_list
(i.e. the return from your set_intersection
function). command
is supposed to equal a function, not a list
, and that's why it is telling you that "function object is not iterable". What it is saying (in clearer terms) is: "you can't assign a list where I expect a function"
QUESTION
Context: I conducted clam surveys at different sites and measured their sizes. The surveys did not include the same total area due to differences in low tides, extent of the clam bed, etc. Therefore, some sites may have high clam density (#/m^2) but low area, therefore the total count at is low, while others may have the opposite characteristics (or any other combination).
I am trying to create a faceted histogram to show size
frequencies at each different site
while removing the effect of the amount of area
surveyed at each site
. Essentially, I want frequencies that reflect each site's density (occurrences per unit area) so I can compare across sites and see overall differences in size distribution AND relative frequency.
Here are some example data:
...ANSWER
Answered 2021-Nov-18 at 01:16Does this do what you want?
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Vulnerabilities
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Install clam
You can use clam like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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