Jupyter notebook to pdf command line

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Jupyter notebook to pdf command line

Jupyter/IPython Notebook Quick Start Guide The Jupyter Notebook App can be launched by clicking on the Jupyter Notebook icon installed by Anaconda in the start menu (Windows) or by typing in a terminal (cmd on Windows): This will launch a new browser window (or a new tab) showing the Notebook Dashboard, a sort of control panel that allows (among other things) to select which notebook to open. When started, the Jupyter Notebook App can access only files within its start-up folder (including any sub-folder). No configuration is necessary if you place your notebooks in your home folder or subfolders. Otherwise, you need to choose a Jupyter Notebook App start-up folder which will contain all the notebooks. See below for platform-specific instructions on how to start Jupyter Notebook App in a specific folder. Copy the Jupyter Notebook launcher from the menu to the desktop. Right click on the new launcher and change the Target field, change %USERPROFILE% to the full path of the folder which will contain all the notebooks. Double-click on the Jupyter Notebook desktop launcher (icon shows [IPy]) to start the Jupyter Notebook App. The notebook interface will appear in a new browser window or tab. A secondary terminal window (used only for error logging and for shut down) will be also opened. To launch Jupyter Notebook App: Click on spotlight, type terminal to open a terminal window. Enter the startup folder by typing cd /some_folder_name. Type jupyter notebook to launch the Jupyter Notebook App The notebook interface will appear in a new browser window or tab. Closing the browser (or the tab) will not close the Jupyter Notebook App. To completely shut it down you need to close the associated terminal. In more detail, the Jupyter Notebook App is a server that appears in your browser at a default address ( ). Closing the browser will not shut down the server. You can reopen the previous address and the Jupyter Notebook App will be redisplayed. You can run many copies of the Jupyter Notebook App and they will show up at a similar address (only the number after ":", which is the port, will increment for each new copy). Since with a single Jupyter Notebook App you can already open many notebooks, we do not recommend running multiple copies of Jupyter Notebook App. When a notebook is opened, its "computational engine" (called the kernel) is automatically started. Closing the notebook browser tab, will not shut down the kernel, instead the kernel will keep running until is explicitly shut down. To shut down a kernel, go to the associated notebook and click on menu File -> Close and Halt. Alternatively, the Notebook Dashboard has a tab named Running that shows all the running notebooks (i.e. kernels) and allows shutting them down (by clicking on a Shutdown button). Download the notebook you want to execute and put it in your notebook folder (or a sub-folder of it). Then follow these steps: Launch the Jupyter Notebook App (see previous section). In the Notebook Dashboard navigate to find the notebook: clicking on its name will open it in a new browser tab. Click on the menu Help -> User Interface Tour for an overview of the Jupyter Notebook App user interface. You can run the notebook document step-by-step (one cell a time) by pressing shift + enter. You can run the whole notebook in a single step by clicking on the menu Cell -> Run All. To restart the kernel (i.e. the computational engine), click on the menu Kernel -> Restart. This can be useful to start over a computation from scratch (e.g. variables are deleted, open files are closed, etc...). More information on editing a notebook: Notebook Basics (or alternate link) Note Save notebooks: modifications to the notebooks are automatically saved every few minutes. To avoid modifying the original notebook, make a copy of the notebook document (menu File -> Make a copy ...) and save the modifications on the copy. Warning Pay attention to not open the same notebook document on many tabs: edits on different tabs can overwrite each other! To be safe, make sure you open each notebook document in only one tab. If you accidentally open a notebook twice in two different tabs, just close one of the tabs. More info on the Jupyter Notebook App environment see References. ? Copyright 2015, Antonino Ingargiola and contributors. Revision 19a9041d. Built with Sphinx using a theme provided by Read the Docs. Normally people run jupyter notebook via browser, but in some situation, we will need to run it from terminal, for example, when running the script takes long time. This post introduces how to run a jupyter notebook script from terminal. Solution I: runipy can do this. runipy will run all cells in a notebook. If an error occurs, the process will stop. $ pip3 install runipy # for python 3.x $ pip install runipy # for python 2.x runipy command-line usages To run a .ipynb file as a script, run: $ runipy MyNotebook.ipynb To save the output of each cell back to the notebook file, run: $ runipy -o MyNotebook.ipynb To save the notebook output as a new notebook, run: $ runipy MyNotebook.ipynb OutputNotebook.ipynb To run a .ipynb file and generate an HTML report, run: $ runipy MyNotebook.ipynb --html report.html Solution II: The latest versions of jupyter comes with the nbconvert command tool for notebook conversion allows us to do this without any extra packages. Just go to your terminal and type: $ jupyter nbconvert --to notebook --execute mynotebook.ipynb --output mynotebook.ipynb This will open the notebook, execute it, capture new output, and save the result in mynotebook.nbconvert.ipynb. By default, nbconvert will abort conversion if any exceptions occur during execution of a cell. If you specify --allow-errors (in addition to the --execute flag) then conversion will continue and the output from any exception will be included in the cell output. if you meet this error, raise exception("Cell execution timed out") $ jupyter nbconvert --to notebook --execute --allow-errors -ExecutePreprocessor.timeout=180 mynotebook.ipynb You can use the ?inplace flag as well: $ jupyter nbconvert --to notebook --execute --inplace mynotebook.ipynb check here for more (updated) usages about nbconvert jupyter command tool. References: Can I run Jupyter notebook cells in commandline? Notebook nbconvert I know the user can convert the notebook into a script and run python ...py in the terminal. Is there any way more convenient to do this task like python ...py to run notebook. Yes, you can directly run a notebook file from the command line. Two main ways I use are nbconvert and papermill. See the third paragraph here for links to documentation for each and some examples. By the way since you mentioned .py files, jupytext can convert a script back to a notebook and run that notebook in one command, here. It also does the conversion from notebook to script on the command line, too. Thanks, I find the solution. Executing notebooks from the command line The same functionality of executing notebooks is exposed through a command line interface or a Python API interface. As an example, a notebook can be executed from the command line with: jupyter nbconvert --to notebook --execute mynotebook.ipynb Is it possible to just execute the notebook, but not generate an output file? I'd like to just time the execution speed of a bunch of notebooks. 1 Like we have an issue to discuss and track this here, in case you'd like to weigh in: 1 Like papermill {test_file_name.ipynb} /dev/null {args...} is a convenient way to do that 2 Likes @MSeal has papermill considered adding a --no-save flag, or something like this? For folks that are not as familiar with coding (or for folks who are on windows), /dev/null may be a bit of a stretch to remember and use. Happy to open an issue to discuss if you think it'd be helpful The library is a little opinionated in that it expects when something goes wrong you want to read the output, so it hasn't been made easy to drop the output. Another option btw is to make the output the same as the input (which will write in place) or to just output to a dummy output path. A --no-save flag could be a decent issue to discuss. The implementation would be a little difficult to make conditional on the --no-save flag since the click configuration as it it's setup to always expect an input and an output path. Happy to discuss more in github if you wanted. 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Where we transfer your data to a Third Party, we will be responsible for the deletion of your data with such Third Parties, as outlined above. Security and Storage of InformationFaculty takes great care in implementing, enforcing and maintaining security policies to help ensure the security of our Services, Sites and our User's Personal Data. You can find out more information about our Security procedures here. Access to your data by Faculty staff and contractorsFaculty takes steps to ensure as far as possible that it's staff are honest, reliable and take all due care in the processing, care and handling of all Data. Faculty limits access to any Personal Data we hold to staff who:Appropriately trained on the requirements applicable to the processing, care and handling of Personal DataAre under confidentiality obligationsAre required to access, process and use the data to carry out the various tasks outlined in the section "How we use your data"Who required access in order for Faculty to fulfill its obligations under this Privacy Policy, Terms or Service and Acceptable Use PolicyCustomer Material in Faculty Platform (with the exception of Customer Material in the form of Registration Information) is hosted on AWS in Ireland which provides advanced security features and is compliant with ISO 27001. All Customer Material is stored with logical separation from information of other customers. Faculty limits access to Customer Material to the following Faculty staff and contractors:Those who require access in order for Faculty to fulfill its obligations under this Privacy Policy, Terms of Service and Acceptable Use PolicyWhere you have requested for us or allowed us to access your account for Support ServicesWhere we are providing essential security and service upgrades, and in such cases the staff have been appropriately trained on the requirements applicable to the processing, care and handling of Personal Data, and are under confidentiality obligations.Notification of breachesFaculty shall notify the User without undue delay, in the event that any Personal Data held by Faculty on the User or on behalf of the User is lost, stolen, or where there has been any unauthorised access to the Personal Data which is likely to result in a high risk to the User's rights or freedoms. Furthermore Faculty undertakes to cooperate with the User in investigating and remedying any such security breach. In any security breach involving Personal Data, Faculty shall immediately take remedial measures, including without limitation, reasonable measures to restore the security of the Personal Data and limit unauthorised or illegal dissemination of the Personal Data or any part thereof. Faculty maintains documentation regarding compliance with the requirements of the law, including but not limited to documentation of any known breaches and holds reasonable insurance policies in connection with data security. Transfer of Data outside of the EEA Personal Data submitted may be transferred by us to Third Parties (as set out under the heading "Sharing with Third Parties"), including service providers that may be situated outside the European Economic Area (EEA) and may be processed by staff operating outside the EEA. Where this is the case we will take reasonable steps to ensure that your privacy rights continue to be protected. In countries where they do not have similar data protection laws to the UK, we will take reasonable steps to ensure that the Third Parties have policies, terms and conditions that provide similar protection to that offered within the EEA as a minimum. By using the Site you agree to this storing, processing and/or transfer.Customer Data is hosted on AWS in Ireland, and is not transferred outside of the EEA without specific and independent permission. Faculty does not transfer any personal data outside of any jurisdiction in a manner incompatible with the requirements of applicable law. Portability of your dataUpon termination of any of our Services for any reason, you may request a copy of your Personal Data, which Faculty will provide in a reasonably acceptable format. Other InformationNotice to End UsersMany of the Services we provide are primarily used by Companies and Organisations. Where we are providing Services to you under a Company or Organisation contract (for example where a company holds a licence for Faculty Platform), any Personal Data held is controlled by your Company or Organisation. Where this is the case, your Personal Data will be subject to the Privacy Policy of your organisation, and questions about your information should be directed to your organisation. Organisation account holders are able to:Enter, modify or delete your Registration Information on your behalfRestrict, suspend or terminate your access to our ServicesAccess and retain your Registration Information and Customer MaterialControl the interaction of third parties with your Customer MaterialWhere the Services are not provided under the control of an Organisation, if you register for our Services with an email address owned by an Organisation, that Organisation may assert control over your Registration Information and Customer Material at a later date. You will be notified if this happens. If you do not want your Organisation to have control over your access to our Services, please register with a personal email address and do not add a Company name to your Registration Information. For all other queries, please contact the person within your Organisation who implements and enforces your Organisation's Privacy Policy. Our Cookie Policy We use cookies and other tracking products to customise our Services, to allow you to login without re-entering your Registration Information, and to understand how our customers use our Services in order to continuously improve them.We use them in the following circumstances:Where they are necessary for you to be able to enable the Services to to provide the feature you have requested (e.g. to login)To customise the functionality where you have selected preferences, for example when you select to turn features off or onTo collect information on how you interact with our Sites and Services, and how you have come to interact with us. For example we use Google Analytics to understand how you came to our Sites and therefore improve our access in the future. We use social media cookies to allow you to follow links on our Sites to our social media accounts, or for you to "like" or "follow" information or articles on our Sites.Most browsers allow you to opt out of accepting cookies through their settings and will also allow you to delete cookies already stored on your computer, however, blocking or deleting all cookies may have a negative impact on your use of our Services, and might prevent them from working altogether.You can opt-out of Google Analytics on all websites by following this link. Children Under 16Our Services are not directed towards children under the age of 16, and therefore (other than in Customer Material controlled by you) we do not hold any Personal Data relating to Children under 16. If you have reason to believe that we may have been provided with Personal Data on a child under 16, please contact us immediately via our contact form. Right to Object You have the right to object to the processing of your Personal data by Faculty:Based on legitimate interestsFor Direct marketingFor the purposes of research and statistics. If you would like to object to the above, you can contact us via our contact page.Report a concernIf you have a concern about our use of your Personal Data or our information rights practices please let us know. You also have the right to lodge a complaint with the Information Commissioner's Office ("ICO"), the UK data protection authority, via this link or by calling 0303 123 1113.Changes to the Privacy PolicyFaculty keeps its Privacy Policy under regular review. If we change our Privacy Policy we will let you know by:Providing notice on our website where the changes are any unsubstantial changes and do not fundamentally alter the spirit of this policy;Sending an email regarding the changes to the email address that you provided in your Registration Information where the changes are substantial. The changes will take effect seven (7) days after notice has been provided.Unless otherwise stated, all changes to this privacy policy are effective as of the stated Last Revised date, and your continued use of the Site and/or Services after the Last Revised date will constitute acceptance of, and agreement to be bound by, those changes. Contact InformationFor any queries or comments on the Policy or its content, or for any other purposes you can contact us by using our contact page or by:Sending an email to: info@faculty.aiWriting to: Operations DepartmentFaculty Science Ltd54 Welbeck StreetLondonW1G 9XSBy telephone on: +44 (0)203 637 9415

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