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astropy / astropy-workshop

Materials for Astropy Workshops
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install problem #35

Closed gclayton18 closed 5 years ago

gclayton18 commented 5 years ago

After the conda environment command, I got this:

pytest-doctestplus-0 | 13 KB | ##################################### | 100%

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/astropy/noarch/astroquery-0.3.9-py_1000.tar.bz2 Elapsed: -

An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way.

When I retried, I got this:

SpecNotFound: Invalid name, try the format: user/package

bsipocz commented 5 years ago

try installing it with pip instead: pip install --pre --upgrade astroquery

bsipocz commented 5 years ago

(it will give you the most recent dev version release, which for astroquery is totally fine to be used)

gclayton18 commented 5 years ago

That worked. Now when I run the Source command, I get: No such file or directory

On Jan 2, 2019, at 10:07 PM, Brigitta Sipocz notifications@github.com wrote:

(it will give you the most recent dev version release, which for astroquery is totally fine to be used)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ he/him/his

bsipocz commented 5 years ago

Well, my answer didn't really address your issue. The connection error must be a transient, so you can try to rerun the conda env create command.

(using pip is totally separate issue, so I'm sorry for the confusion).

gclayton18 commented 5 years ago

Then I get the same error: SpecNotFound: Invalid name, try the format: user/package

On Jan 2, 2019, at 10:37 PM, Brigitta Sipocz notifications@github.com wrote:

Well, my answer didn't really address your issue. The connection error must be a transient, so you can try to rerun the conda env create command.

(using pip is totally separate issue, so I'm sorry for the confusion).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ he/him/his

JuanCab commented 5 years ago

I think that SpecNotFound error means it is not finding the expected environment.yml file. Did you type the command conda env create -n astropy-workspace --file environment.yml from a command line when your command line after changing directory to the directory containing environment.yml?

For example, if you are on a mac and your astropy-workshop directory was in your home directory, you should open the terminal and type the following 2 commands:

cd ~/astropy-workshop/00-Install_and_Setup
conda env create -n astropy-workspace --file environment.yml

In windows, you would open the command line and type these 2 commands:

cd astropy-workshop\00-Install_and_Setup
conda env create -n astropy-workspace --file environment.yml
gclayton18 commented 5 years ago

That was a success.

What directory should I be in when I give the source command. I am getting:

activate: No such file or directory

On Jan 2, 2019, at 11:55 PM, Juan Cabanela notifications@github.com wrote:

I think that SpecNotFound error means it is not finding the expected environment.yml file. Did you type the command conda env create -n astropy-workspace --file environment.yml from a command line when your command line after changing directory to the directory containing environment.yml? For example, if you are on a mac and your astropy-workshop directory was in your home directory, then you would type:

cd ~/astropy-workshop/00-Install_and_Setup conda env create -n astropy-workspace --file environment.yml

In windows, you would type:

cd astropy-workshop\00-Install_and_Setup conda env create -n astropy-workspace --file environment.yml

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ he/him/his

JuanCab commented 5 years ago

the conda activate astropy-workshop command should work regardless of the directory you are in. Did you remember the conda in front?

gclayton18 commented 5 years ago

Like this?

conda source activate astropy-workshop

I get:

CommandNotFoundError: No command 'conda source'.

On Jan 3, 2019, at 7:19 AM, Juan Cabanela notifications@github.com wrote:

the conda activate astropy-workshop command should work regardless of the directory you are in. Did you remember the conda in front?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ he/him/his

JuanCab commented 5 years ago

Not quite, you want conda activate astropy-workshop, no "source".

gclayton18 commented 5 years ago

FYI. The install instructions say:

% conda env create -n astropy-workshop --file environment.yml % source activate astropy-workshop

On Jan 3, 2019, at 7:29 AM, Juan Cabanela notifications@github.com wrote:

Not quite, you want conda activate astropy-workshop, no "source".

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/astropy/astropy-workshop/issues/35#issuecomment-451129892, or mute the thread https://github.com/notifications/unsubscribe-auth/AOj-Eq_z1E4Cam6Luu8no5o_dISnNeJBks5u_feSgaJpZM4ZngiI.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ http://morpheus.phys.lsu.edu/~gclayton/he/him/his

JuanCab commented 5 years ago

You are correct, the installation instructions are in error, trying to get a fix in.

gclayton18 commented 5 years ago

Meanwhile, when I try to activate, I get the instructions below. I have followed them but nothing changes.

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. If your shell is Bash or a Bourne variant, enable conda for the current user with

$ echo ". /Users/gclayton/miniconda3/etc/profile.d/conda.sh" >> ~/.bash_profile

or, for all users, enable conda with

$ sudo ln -s /Users/gclayton/miniconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh

The options above will permanently enable the 'conda' command, but they do NOT put conda's base (root) environment on PATH. To do so, run

$ conda activate

in your terminal, or to put the base environment on PATH permanently, run

$ echo "conda activate" >> ~/.bash_profile

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in your ~/.bash_profile file. You should manually remove the line that looks like

export PATH="/Users/gclayton/miniconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^

On Jan 3, 2019, at 7:38 AM, Juan Cabanela notifications@github.com wrote:

You are correct, the installation instructions are in error, trying to get a fix in.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/astropy/astropy-workshop/issues/35#issuecomment-451131709, or mute the thread https://github.com/notifications/unsubscribe-auth/AOj-ElDz5ezFhdBIRIw8hqHqmfeDO2gLks5u_fmzgaJpZM4ZngiI.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ http://morpheus.phys.lsu.edu/~gclayton/he/him/his

JuanCab commented 5 years ago

OK, unless you previously installed conda in the past, the only thing you should have to do is:

echo ". /Users/gclayton/miniconda3/etc/profile.d/conda.sh" >> ~/.bash_profile

If that doesn't work, it may indicate you have a more complicated bash environment and we may need to check your setup when you arrive at the workshop.

gclayton18 commented 5 years ago

I have installed anaconda in the past. I know this has been painful. I appreciate your help. I just made new .bash_profile and .bashrc files and ran the command below with no effect. I assume you have run out of ideas.

On Jan 3, 2019, at 7:56 AM, Juan Cabanela notifications@github.com wrote:

OK, unless you previously installed conda in the past, the only thing you should have to do is:

echo ". /Users/gclayton/miniconda3/etc/profile.d/conda.sh" >> ~/.bash_profile

If that doesn't work, it may indicate you have a more complicated bash environment and we may need to check your setup when you arrive at the workshop.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/astropy/astropy-workshop/issues/35#issuecomment-451135439, or mute the thread https://github.com/notifications/unsubscribe-auth/AOj-EkzHzb58WGF2nqSaOUM6zwPAMCJIks5u_f32gaJpZM4ZngiI.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ http://morpheus.phys.lsu.edu/~gclayton/he/him/his

JuanCab commented 5 years ago

I suspect your previous anaconda installation is mucking things up. Does your new .bash_profile just contain the single line

. /Users/gclayton/miniconda3/etc/profile.d/conda.sh

? If so, open a NEW terminal window (to re-launch bash) and see if it works.

gclayton18 commented 5 years ago

Yes just that line. When I open a new widow and run activate, it still says my bash is not configured properly.

On Jan 3, 2019, at 8:11 AM, Juan Cabanela notifications@github.com wrote:

I suspect your previous anaconda installation is mucking things up. Does your .bash_profile just contain the single line

. /Users/gclayton/miniconda3/etc/profile.d/conda.sh

? If so, open a NEW terminal window (to re-launch bash) and see if it works.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/astropy/astropy-workshop/issues/35#issuecomment-451138696, or mute the thread https://github.com/notifications/unsubscribe-auth/AOj-EufpVr3-IGrkjEiNvJ1Z0bV8giEYks5u_gF3gaJpZM4ZngiI.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ http://morpheus.phys.lsu.edu/~gclayton/he/him/his

JuanCab commented 5 years ago

Well, look for me Sunday morning (or Saturday night maybe) and we can try to resolve this. I’ll send you an email shortly with my contact info.

JuanCab commented 5 years ago

We can probably close this issue!

gclayton18 commented 5 years ago

Yes. Thanks.

On Jan 3, 2019, at 11:19 AM, Juan Cabanela notifications@github.com wrote:

We can probably close this issue!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/astropy/astropy-workshop/issues/35#issuecomment-451193843, or mute the thread https://github.com/notifications/unsubscribe-auth/AOj-EmkXLSrUTAsLFqRAjNuRy9gsCkDnks5u_i2HgaJpZM4ZngiI.

Geoffrey C. Clayton Ball Family Distinguished Professor, Physics & Astronomy Nicholson 233-A Louisiana State University Baton Rouge, LA 70803

Phone: 225-578-8275 Cell: 225-405-1617 http://morpheus.phys.lsu.edu/~gclayton/ http://morpheus.phys.lsu.edu/~gclayton/he/him/his